Methods for assessing rna patterns

ABSTRACT

Methods and compositions for the characterizing of cancers by assessing RNA levels, such as determining an RNA pattern, are provided herein. The diagnosis, prognosis, monitoring and treatment or a cancer can be determined by detecting one or more RNAs, such as microRNAs.

CROSS-REFERENCE

This application claims the benefit of U.S. Provisional Application Nos.61/109,742, filed Oct. 30, 2008: 61/112,571, filed Nov. 7, 2008;61/114,045, filed Nov. 12, 2008; 61/114,058, filed Nov. 12, 2008;61/114,065, filed Nov. 13, 2008; 61/151,183, filed Feb. 9, 2009; CanisMPI docket No. 2310 (WSGR Reference No. 37901-706.103) titled “MicroRNAProfiles in Exosomes Derived From Prostate Adenocarcinomas,” filed Oct.2, 2009; 61/250,454, filed Oct. 9, 2009, and 61/253,027 filed Oct. 19,2009, each of which is incorporated herein by reference in its entirety.

BACKGROUND

Patient healthcare can be greatly improved my providing improved methodsof characterizing a disease or condition by providing a diagnosis,prognosis, or treatment selection for the disease or condition. Thedisease or condition can be detected earlier, or its stage determined todetermine what type of treatment should be selected. The disease orcondition can be a cancer, such as an epithelial cancer or carcinoma.There are different types of epithelial cells and these can develop intodifferent types of cancer. For example, epithelial cells can constitutea flat surface covering of cells called squamous cells. Additionally,epithelial cells can take a glandular form called adenomatous cells.Also, epithelial cells can form a stretchy layer called transitionalcells. Carcinomas make up about 85% of all cancers, and include breast,prostate, lung, colorectal, bladder and ovarian cancers.

Epithelial based cancers usually result in a solid mass or a tumor fromwhich cancer cells migrate throughout the body eventually residing inother locations to establish secondary tumors or metastases. One of themajor therapies for cancers resulting in solid tumors is the surgicalremoval or oblation of the tumor by physical or chemical means. After acancer is removed from a subject, for example by surgical removal, themonitoring or detection of recurrence of the cancer at the same orsecondary sites, can be indicated, so that additional therapies can beemployed for treatment should that occur. Likewise, some means ofmonitoring the success of cancer therapy can be indicated during thetreatment phase in order to determine if the therapy is being successfulor not and in order to appropriately adapt the therapy accordingly.

There is a need for methods of characterizing cancers, such asepithelial cancers. For example, despite the contribution that theProstate Specific Antigen (PSA) test has made to the management ofprostate cancer, it is plagued by significant shortcomings which resultfrom the antigen being specific for prostate tissue and not for prostatecancer. While the test is highly specific for the PSA antigen, not allprostate cancers release excessive levels of the antigen into the serum.This results in the lack of clinical sensitivity and results in frequentmissing of clinically significant cancers with routine PSA examinations.

A normal PSA value is currently considered to be less than 4.0 ng/mL. Itis believed that at least 20% of men with significant prostate cancersmay have a PSA value less than 4.0 ng/mL. However, since PSA is made bynormal, indolent hyperplastic, pre-malignant and malignant tissue, thefinding of an elevated PSA (greater than 4.0 ng/mL) does not alwaysindicate cancer. If the serum PSA is in the range of 4.0 to 10 ng/mLthere is only a 25-30% chance of finding prostate cancer even throughthe use of repeated and more thorough biopsies (10-12 cores). Thefinding of an elevated PSA value frequently results in the subjectundergoing an uncomfortable and potentially dangerous transrectalbiopsy. It is not uncommon for a man with a significantly elevated PSAto undergo two or more biopsies, in an attempt to find the cause of theelevated serum PSA.

Thus, there is a need for improved methods for characterizing cancer.Provided herein are methods and systems that meet this need, andprovides related advantages as well.

INCORPORATION BY REFERENCE

All publications and patent applications mentioned in this specificationare herein incorporated by reference to the same extent as if eachindividual publication or patent application was specifically andindividually indicated to be incorporated by reference.

SUMMARY

Provided herein are methods for characterizing a disease or condition bydetecting or assessing an RNA or RNA pattern. Characterizing a conditioncan include diagnosing, prognosing, monitoring, selecting a treatment,or classifying a disease or condition, such as a cancer. The cancer canbe an epithelial cancer, such as a breast, brain, pancreas, bone, liver,stomach, lung, colorectal, bladder, prostate or ovarian cancer. The RNApattern can comprise detecting miRNAs, such as the expression level ofmiRNAs.

In some embodiments, the method includes characterizing a cancer in asubject comprising: determining a miRNA pattern in a biological sampleof said subject, wherein the miRNA pattern comprises an expression levelof each of a plurality of miRNAs in said sample. In some embodiments,characterizing is with increased sensitivity as compared tocharacterization by detecting an expression level of less than each ofthe plurality of miRNAs. The miRNAs can be selected from Table 1.

Also provided are methods of classifying a cancer, such as benign ormalignant, and methods of determining if a solid tissue biopsy should beobtained after an initial analysis of a non-biopsy sample. The methodcan also further include selecting a therapy or treatment regimen basedon the classification or results of the biopsy. Classifying a cancer ordetermining if a biopsy should be obtained can include determining theexpression level of a miRNA, such as the copy number of the miRNA permicroliter. The method can also include determining the expression levelof PSA, such as the protein level, or a PCA3 score, which is the ratiobetween the PCA3 expression level and PSA expression level of abiological sample. The method can also include determining a productvalue to characterize a cancer. The product value can be determined bymultiplying the expression level of a miRNA, such as miR-141, with thelevel of PSA. For example, the copy number per microliter of miRNA canbe multiplied by the nanograms per/

Also provided herein is a method of characterizing a cancer, such asprostate cancer, by determining the expression level of one or moremiRNAs, such as miR-141, miR-629, miR-671-3p, miR-9, miR-491, miR-182,miR125a-3p, miR-324-5p, miR-148b, miR-222, or miR-370.

The RNA or RNA pattern can also be used in conjunction with othernon-RNA biomarkers to characterize a cancer.

BRIEF DESCRIPTION OF THE DRAWINGS

The details of one or more exemplary embodiments are set forth in theaccompanying drawings and the description below. Other features,objects, and advantages will be apparent from the description anddrawings, and from the claims.

FIG. 1: illustrates the results of gene analysis of prostate cancersamples. A) In the first study, fourteen prostate cancer tissues wereanalyzed for gene expression profiles on the Agilent 44K ExpressionProfile platform. The genes with most commonly overexpressed are listed.B) In a separate study, a set of 6 prostate cancers was analyzed for theexpression level of genes by using the same platform as in A). The top100 expressing genes were identified. Those genes that listed in the top100 for 5/6 and 6/6 of the prostate cancers are listed. C) Prostatecancer samples from 22 individuals were examined by immunohistochemistry(IHC) for the overexpression of genes. Those genes that wereoverexpressed in at least 10 of the 22 samples are listed.

FIG. 2 illustrates expression profiles for 6 prostate cancer samples.This figure shows the expression profile from the Agilent gene chipanalysis on the 6 prostate cancer samples with the gene names listed onthe right. Dark coloring or shading indicates high expression levels.

FIG. 3 illustrates analysis for cancer samples. A set of 6 prostatecancers was analyzed for the expression level of genes and the top 100expressing genes was listed. Those genes that listed in the top 100 for5/6 and 6/6 of the prostate cancers are listed in FIG. 1B.

FIG. 4 is a graph illustrating the frequency of a miRNA (listed alongthe x-axis), by analyzing the most frequently over-expressed genes inthe prostate cancer samples in a database by both immunohistochemistry(IHC) and gene expression profiling on the Agilent 44K chip, searching apublicly available mRNA database for microRNAs known to be related tothose genes (for example, as http://www.microRNA.org), and ranking themiRNAs by frequency observed.

FIG. 5 is a table showing the product of the PSA value and the level ofmiR-141 for 25 subjects with confirmed prostate cancer versus 25subjects without prostate cancer. A) lists the miR-141 copies, the PSAlevels, and product values for the prostate cancer subjects and normalsubjects. B) is a table showing the mean values, standard deviation,confidence level and the upper and lower levels of miR-141 and PSA inthe normal subjects and the prostate cancer subjects (PrCa).

FIG. 6 is a block diagram showing a representative logic device forusing with one or more methods disclosed herein, such as for receivingdata, determining RNA expression levels, calculating product values,characterizing cancers, transmitting the results or data, and outputtingthe results.

DETAILED DESCRIPTION

Provided herein are methods of characterizing a condition or disease byassessing an RNA or RNA pattern in a biological sample from a subject.Characterizing a disease or condition can include detecting, diagnosing,prognosing, or monitoring a disease or condition. Characterizing canalso include detecting or diagnosing (including pre-symptomatic earlystage detecting), determining the prognosis or theranosis, ordetermining the stage or progression of a disease or condition. Alsoincluded is determining the drug efficacy or selecting a treatment for adisease or condition and prediction and likelihood analysis ofprogression of the disease or condition, such as recurrence, spread orrelapse of a disease or condition based on an RNA or a plurality ofRNAs, such as an RNA pattern. Characterizing a disease or condition canalso include classifying the disease or condition. Furthermore, the RNAor RNA pattern determined in a sample can be used to determine whetherto obtain a second sample, such as a biopsy for further analysis.

The disease or condition that can be characterized according to themethods and compositions disclosed herein can be a cancer. Examples ofcancer include bladder cancer; esophageal cancer; lung cancer; stomachcancer; kidney cancer; cervical cancer; ovarian cancer; breast cancer;lymphoma; Ewing sarcoma; hematopoietic tumors; solid tumors; gastriccancer; colorectal cancer; brain cancer; epithelial cancer;nasopharyngeal cancer; uterine cancer; hepatic cancer; head-and-neckcancer; renal cancer; male germ cell tumors; malignant mesothelioma;myelodysplastic syndrome; pancreatic or biliary cancer; prostate cancer;thyroid cancer; urothelial cancer; renal cancer; Wilm's tumor; smallcell lung cancer; melanoma; skin cancer; osteosarcoma; neuroblastoma;leukemia (acute lymphocytic leukemia, acute myeloid leukemia, chroniclymphocytic leukemia); glioblastoma multiforme; medulloblastoma;lymphoplasmacytoid lymphoma; or rhabdomyosarcoma. The cancer can be anepithelial cancer. Epithelial cancers are cancers of skin tissue thatcovers and lines the body, such as breast, brain, liver, pancreas,stomach, bone, colorectal, bladder, ovarian or lung cancer. In someembodiments, the cancer is prostate cancer.

Samples

One or more RNAs can be assessed from a biological sample obtained froma subject. The biological sample may be of any biological tissue, fluid,or cell from the subject. The sample can be solid or fluid. The samplecan be a heterogeneous cell population. The sample can be sputum, blood,blood cells (e.g., white cells), a biopsy, urine, peritoneal fluid,pleural fluid, or cells derived therefrom. The biopsy can be a fineneedle aspirate biopsy, acore needle biopsy, a vacuum assisted biopsy,an open surgical biopsy, a shave biopsy, a punch biopsy, an incisionalbiopsy, a curettage biopsy, or a deep shave biopsy. Biological samplesmay also include sections of tissues, such as frozen sections orformalin fixed sections taken for histological purposes. A sample can bea tumor tissue, tissue surrounding a tumor, or non-tumor tissue.

The subject can include mammals such as bovine, avian, canine, equine,feline, ovine, porcine, or primate animals (including humans andnon-human primates). In some embodiments, the subject is a human of aspecific gender or age. For example, the age of the subject can be atleast about 30, 35, 40, 45, 50, 55, or 60 years of age. To characterizeprostate cancer, the subject may be a male human of at least 50 years ofage. The subject can have a pre-existing disease or condition, or afamily history of a pre-existing disease or condition, such as cancer.Alternatively, the subject may not have any known pre-existingcondition. The subject may also be non-responsive to an existing or pasttreatment, such as a treatment for cancer.

Exosomes

In some embodiments, one or more RNAs disclosed herein is assessed fromexosomes of a biological sample. Exosomes are vesicles that are releasedinto the extracellular environment from a variety of different cellssuch as but not limited to dendritic cells, tumor cells, lymphoid cells,mesothelial cells, epithelial cells, or cells from different tissues ororgans. An exosome is created intracellularly when a segment of the cellmembrane spontaneously invaginates and is ultimately exocytosed (Kelleret al., Immunol. Leu. 107 (2): 102-8 (2006)). Exosomes may also bereferred to as microvesicles, nanovesicles, vesicles, dexosomes, blebs,prostasomes, microparticles, intralumenal vesicles, endosome-likevesicles or exocytosed vehicles.

Exosomes can also include any shed membrane bound particle that isderived from either the plasma membrane or an internal membrane.Exosomes may further include cell-derived structures bounded by a lipidbilayer membrane arising from both herniated evagination (blebbing)separation and scaling of portions of the plasma membrane or from theexport of any intracellular membrane-bounded vesicular structurecontaining various membrane-associated proteins of cellular origin,including surface-bound molecules derived from the host circulation thatbind selectively to the tumor-derived proteins together with moleculescontained in the exosome lumen, including but not limited totumor-derived microRNAs, mRNAs, and intracellular proteins. Exosomes canalso include membrane fragments.

The secretion of exosomes by tumor cells and their implication in thetransport of proteins and nucleic acids (eg. micro RNAs) suggest theirparticipation in pathological processes. Exosomes have been found in anumber of body fluids including but not limited to blood plasma,bronchoalveolar lavage fluid and urine, indicating relevance in vivo.Exosomes have been suggested to have a number of different functions andare believed to take part in the communication between cells, as well astransport vehicles for proteins, RNAs, DNAs, viruses, and prions.

Assessing one or more RNAs from an exosome can provide improved assaysensitivity and specificity for cancer detection, such as for theprognosis, monitoring, disease staging, and therapeutic decision-makingof the cancer.

Assessing one or more RNAs to characterize a cancer can includedetecting the amount of exosomes with a specific RNA or a specific RNApattern. In other embodiments, detecting an RNA or RNA pattern of anexosome can be used to characterize a cancer. The exosome for analysiscan be in a heterogeneous population of exosomes or a homogeneous, orsubstantially homogeneous, population of exosomes. The exosome can bepurified or concentrated prior to analyzing the exosome. Exosomes may beconcentrated or isolated from a biological sample using size exclusionchromatography, density gradient centrifugation, differentialcentrifugation, nanomembrane ultrafiltration, immunoabsorbent capture,affinity purification, microfluidic separation, or combinations thereof.For example, size exclusion chromatography such as gel permeationcolumns, centrifugation or density gradient centrifugation, andfiltration methods can be used. For example, exosomes can be isolated bydifferential centrifugation, anion exchange and/or gel permeationchromatography (for example, as described in U.S. Pat. Nos. 6,899,863and 6,812,023), sucrose density gradients, organelle electrophoresis(for example, as described in U.S. Pat. No. 7,198,923), magneticactivated cell sorting (MACS), or with a nanomembrane ultrafiltrationconcentrator. Various combinations of isolation or concentration methodscan be used.

Binding agents, or capture agents, can be used to isolate exosomes bybinding to exosomal components. A binding or capture agent may be usedafter the exosomes are concentrated or isolated from a biologicalsample. For example, exosomes are first isolated from a biologicalsample before exosomes with a specific biomarker are isolated using abinding agent for the biomarker. Thus, exosomes with the specificbiomarker are isolated from a heterogeneous population of exosomes.Alternatively, a binding agent may be used on a biological samplecomprising exosomes without a prior isolation step of exosomes. Forexample, a binding agent is used to isolate exosomes with a specificbiomarker from a biological sample.

The binding agent can be, but not limited to, DNA, RNA; aptamers,monoclonal antibodies, polyclonal antibodies, Fabs, Fab′, single chainantibodies, synthetic antibodies, aptamers (DNA/RNA), peptoids, zDNA,peptide nucleic acids (PNAs), locked nucleic acids (LNAs), lectins,synthetic or naturally occurring chemical compounds (including but notlimited to drugs, labeling reagents), or dendrimers.

In some embodiments, prostate specific exosomes, or prostatsomes, suchas from a blood sample or urine is used for assessing one or more RNAsto characterize a cancer. Exosomes that are derived from a prostatecancer cells can be isolated using an antibody, or any other bindingagent, for one or more antigens that are specific for a cell of prostatecancer origin such as PSA, TMPRSS2, FASLG, TNFSF10, PSMA, NGEP, Il-7R1,CSCR4, CysLTIR, TRPM8, Kv1.3, TRPV6, TRPM8, PSGR, MISIIR, galectin-3,PCA3, TMPRSS2:ERG, fragments thereof, any combination thereof, or anycombination of antigens that are specific for prostate cancer cells. Thebinding agent can be PSA, PSMA, mAB 5D4, XPSM-A9, XPSM-A10, Galectin-3,E-selectin, Galectin-1, E4 (IgG2a kappa), or any combination thereof.The binding agent or capture agent used to isolate an exosome can alsobe an agent that binds exosomal “housekeeping proteins,” such as CD63,CD9, CD81, or Rah-5b, or a binding agent for EpCAM is used to isolateexosomes.

RNAs

Assessment of any species of RNA can be used to characterize a diseaseor condition, such as cancer. The RNA can be microRNA (miRNA or miR),mRNA, small nuclear RNA, siRNA, small nucleolar RNA, or ribosomal RNA.The RNA pattern can comprise any RNA species, such as a microRNA (miRNAor miR), mRNA, small nuclear RNA, small nucleolar RNA, ribosomal RNA, orany combination thereof. The RNA pattern can comprise a single speciesof RNA or any combination of species, such as a miRNA and a mRNA. Theassessment of an RNA can include determining or detecting the expressionlevel of an RNA, such as the overexpression or underexpression ascompared to a control, the absence or presence of an RNA, or the copynumber of the RNA, such as copy numbers per microliter of sample, suchas the copy number per microliter of plasma, or the copy number permicroliter of serum. In some embodiments, assessing an RNA is detectingor determining the sequence of an RNA, or detecting a mutation orvariant of an RNA.

A plurality of RNAs can be used to characterize a disease or condition,such as cancer. For example, an RNA pattern can comprise 2 or moredifferent RNAs, such as at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25,30, 40, 50, 60, 70, 80, 90, 100, 1000, 2500, 5000, 7500, 10,000,100,000, 150,000, 200,000, 250,000, 300,000, 350,000, 400,000, 450,000,500,000, 750,000, or 1,000,000 different RNAs. In some embodiments, theRNA pattern comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25,30, 40, 50, 60, 70, 80, 90, 100, 1000, 2500, 5000, 7500, 10,000,100,000, 150,000, 200,000, 250,000, 300,000, 350,000, 400,000, 450,000,500,000, 750,000, or 1,000,000 different miRNAs. The RNA pattern canalso comprise one or more different miRNAs in combination with otherspecies of RNAs, such as mRNA.

Also provided herein are methods of assessing one or more RNAs that canbe used to diagnose a cancer. Diagnosis can include a negativediagnosis, such as no cancer is present. In other embodiments, diagnosismay include identifying the stage of a cancer, or the pre-symptomaticstages of a cancer. The one or more RNAs can also be used to provide aprognosis of a cancer, such as providing the risk or susceptibility ofhaving a cancer or the aggressiveness or malignancy of a cancer.

Assessing one or more RNAs in sample can also be used to select a cancertherapy. Detection of one or more RNAs can be used to determine theefficacy of a cancer therapy or treatment, such as the relativeimprovement or deterioration of the subject's condition. Assessing oneor more RNAs from samples of patients treated with effective therapiesor non-effective therapies can be determined and used as a reference forselecting a therapy for a subject. In another embodiment, as a subject'scancer becomes progressively worse or better, the level of one or moreRNAs may change, and compared to a reference of one or more RNAs frompatients that were in a worse or better stage of the cancer.

The treatment or therapeutic selected based on one or more RNAs can be atreatment for cancer, such as an anti-cancer regimen or treatment thatis selected from one or more of the following: vaccination, anti-growthfactor or signal transduction therapy, radiotherapy, endocrine therapy,or human antibody therapy chemotherapy. The treatment can comprise a DNAdamaging agent, topoisomerase inhibitor, mitotic inhibitor or acombination thereof. Many chemotherapeutics are presently known in theart and can be used in combination with the one or more compoundsdescribed herein. For example, the chemotherapeutic can be selected fromthe group consisting of: a mitotic inhibitor, alkylating agent,anti-metabolite, intercalating antibiotic, growth factor inhibitor, cellcycle inhibitor, enzyme, topoisomerase inhibitor, biological responsemodifier, anti-hormone, angiogenesis inhibitor, and anti-androgen. Asused herein, cancer treatment, cancer therapy and the like encompassestreatments such as surgery, such as cutting, abrading, ablating (byphysical or chemical means, or a combination of physical or chemicalmeans), suturing, lasering or otherwise physically changing body tissuesand organs), radiation therapy, administration of chemotherapeuticagents and combinations of any two or all of these methods. Combinationtreatments may occur sequentially or concurrently. Treatments, such asradiation therapy and/or chemotherapy, that are administered prior tosurgery, are referred to as neoadjuvant therapy. Treatments, such asradiation therapy and/or chemotherapy, administered after surgery isreferred to herein as adjuvant therapy. Examples of surgeries that maybe used for prostate cancer treatment include, but are not limited toradical prostatectomy, cryotherapy, transurethral resection of theprostate, and the like.

Detection of one or more RNAs can also be used to determine the efficacyof a cancer therapy or treatment, such as the relative improvement ordeterioration of the subject's condition. One or more RNAs for patientsbeing treated for cancer can be determined and correlated to theimprovement or beneficial efficacy, which is then used as a reference.For example, the improvement or beneficial efficacy can typically beassessed by determining if one or more of the following events hasoccurred: decreased or tumor size, decreased or tumor cellproliferation, decreased or numbers of cells, decreased orneovascularization and/or increased apoptosis. One or more of theseoccurrences may, in some cases, result in partial or total eliminationof the cancer and prolongation of survival of the subject.Alternatively, for terminal stage cancers, treatment may result instasis of disease, better quality of life and/or prolongation ofsurvival. The converse result and/or stasis in any of those events canindicate inefficacy of treatment or therapy. Other methods of assessingtreatment are known in the art and contemplated herein. Differentassessments can be correlated with different RNAs or RNA patterns.

Assessing one or more RNAs can also be used monitor the progress of ananti-cancer treatment regimen or treatment in a subject, or therecurrence of a cancer. For example, the RNA or RNA patterns at varioustimepoint throughout a treatment. The RNA or RNA pattern can also beused to monitor a subject for the spread of a cancer. For example,miR-141 can be used for detecting the recurrence of colorectal cancer.Currently, colorectal cancer recurrence is measured by the level of theantigen CEA (carcino embryonic antigen). However, CEA can haveconfounding issues when used alone. For example, not all metastaticcolorectal tumors express CEA, creating the need for additional markers,like miR-141. Similar issues are known for other single antigen testsfor epithelial based cancers such as ovarian, breast, lung and bladdercancer.

Recurrence can be determined by periodically obtaining sample from asubject and monitoring the RNA or RNA pattern periodically from a sampleof the subject. For example, an epithelial cancer has recurred if themiR-141 in the periodic blood samples shows a steady change in amount oris significantly elevated when compared to a miR-141 amount in a controlsample that corresponds to subjects without epithelial cancer. In oneembodiment, after a cancer is removed from a subject, for examplesurgically, the subject is monitored and through assessing an RNA or RNApattern, the recurrence of the cancer at the same or secondary site canbe identified so that additional therapies can be employed fortreatment. In another embodiment, a subject is monitored during thetreatment phase by having samples taken before and during treatment foranalysis of an RNA or RNA pattern. Based on the RNA or RNA pattern, thetherapy can be determined successful or not, if the therapy should beadapted or if the patient should try another therapy.

Classification

In another embodiment, assessing one or more RNAs can be used toclassify or stage a cancer. The classification and staging may also beused to assess treatment of cancers.

For example, the cancer can be classified based on the TNMclassification of malignant tumors. This cancer staging system can beused to describe the extent of cancer in a subject's body. T describesthe size of the tumor and whether it has invaded nearby tissue, Ndescribes regional lymph nodes that are involved, and M describesdistant metastasis. TNM is maintained by the International Union AgainstCancer (UICC) and is used by the American Joint Committee on Cancer(AJCC) and the International Federation of Gynecology and Obstetrics(FIGO). One would understand that not all tumors have TNMclassifications such as, for example, brain tumors. Generally, T(a,is,(0); 1-4) is measured as the size or direct extent of the primarytumor. N (0-3) refers to the degree of spread to regional lymph nodes:N0 means that tumor cells are absent from regional lymph nodes, N1 meansthat tumor cells spread to the closest or small numbers of regionallymph nodes, N2 means that tumor cells spread to an extent between N1and N3; N3 means that tumor cells spread to most distant or numerousregional lymph nodes, M (0/1) refers to the presence of metastasis: M0means that no distant metastasis are present; M1 means that metastasishas occurred to distant organs (beyond regional lymph nodes). Otherparameters may also be assessed. G (1-4) refers to the grade of cancercells (i.e., they are low grade if they appear similar to normal cells,and high grade if they appear poorly differentiated). R (0/1/2) refersto the completeness of an operation (i.e., resection-boundaries free ofcancer cells or not). L (0/1) refers to invasion into lymphatic vessels.V (0/1) refers to invasion into vein. C (1-4) refers to a modifier ofthe certainty (quality) of V.

The methods also include classifying a prostate tumor based on theGleason scoring system. The Gleason scoring system is based onmicroscopic tumor patterns assessed by a pathologist while interpretingthe biopsy specimen. When prostate cancer is present in the biopsy, theGleason score is based upon the degree of loss of the normal glandulartissue architecture (i.e. shape, size and differentiation of theglands). The classic Gleason scoring system has five basic tissuepatterns that are technically referred to as tumor “grades.” Themicroscopic determination of this loss of normal glandular structurecaused by the cancer is represented by a grade, a number ranging from 1to 5, with 5 being the worst grade. Grade 1 is typically where thecancerous prostate closely resembles normal prostate tissue. The glandsare small, well-formed, and closely packed. At Grade 2 the tissue stillhas well-formed glands, but they are larger and have more tissue betweenthem, whereas at Grade 3 the tissue still has recognizable glands, butthe cells are darker. At high magnification, some of these cells in aGrade 3 sample have left the glands and are beginning to invade thesurrounding tissue. Grade 4 samples have tissue with few recognizableglands and many cells are invading the surrounding tissue. For Grade 5samples, the tissue does not have recognizable glands, and are oftensheets of cells throughout the surrounding tissue.

For example, after an initial analysis of a biological sample for one ormore RNAs, based on the levels of one or more RNAs, a second analysiscan be performed by a pathologist, where the pathologist determines aGleason score for the sample. A biological fluid, such as urine can beanalyzed for one or more RNAs prior to obtaining a biopsy to determine aGleason score for a subject.

Assessing one or more RNAs can also be used to classify a cancer asmalignant (e.g., aggressive) or benign (e.g., indolent). For example, amiRNA pattern can be determined for a biological sample and used toclassify whether a cancer is aggressive or indolent. For example, themethods disclosed herein can be used to classify prostate cancer, bydistinguishing between benign (e.g., indolent) and malignant (e.g.,aggressive) prostate cancers.

Classification can be based on the amount or level of an RNA, or on thelevel of each of a plurality of RNAs. For example, the classificationfor a cancer is indolent epithelial cancer when the level of an RNAs,such as miRNA, is less than about 3000 copies per microliter of sample,for example, a serum sample. The classification for a cancer can bebenign if the RNA level is between about 1000 and about 3000 copies permicroliter, such as less than about 1100, 1200, 1300, 1400, 1500, 1600,1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800,2900 or 3000. In some embodiments, a cancer is classified as benign whenthe expression level of a subset of RNAs that are detected is less thanabout 3000 copies per microliter of sample. In other embodiments, acancer is classified as benign when the expression level of a subset ofRNAs that are detected is between about 1000 and about 3000 copies permicroliter of sample, such as less than about 1100, 1200, 1300, 1400,1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600,2700, 2800, 2900 or 3000 copies per microliter.

In some embodiments, the classification of an epithelial cancer, such asprostate cancer, is malignant when the level of the RNA, such as miRNA,is at least about 9000, such as between about 9000 and about 26000copies per microliter of sample, such as serum sample. For example, ifthe sample has at least about 9100, 9200, 9300, 9400, 9500, 9600, 9700,9800, 9900, 10000, 10100, 10200, 10300, 10400, 10500, 10600, 10700,10800, 10900, 11000, 11100, 11200, 11300, 11400, 11500, 11600, 11700,11800, 11900, 12000, 12100, 12200, 12300, 12400, 12500, 13000, 13500,14000, 14500, 15000, 15500, 16000, 16500, 17000, 17500, 18000, 18500,19000, 19500, 20000, 20500, 21000, 21500, 22000, 22500, 23000, 23500,24000, 24500, 25000, or 25,500 copies per microliter.

Additional Biological Samples

The assessment of one or more RNAs can be performed on a sample obtainednon-invasively, such as a urine sample or blood sample, to characterizea disease or condition, such as cancer. This can reduce the number ofunnecessary biopsies or other invasive procedures for a subject. Thus,in some embodiments, assessing one or more RNAs is performed on a firstsample from a subject. Based on the assessment of the one or more RNAsperformed on the first sample, a second sample from the subject can beobtained for analysis to characterize a cancer. For example, the secondsample can be of a different sample type from the first sample type andused for a different type of analysis, such as for histologicalexamination, such as immunohistochemistry (IHC), in situ hybridization(such as fluorescent in situ hybridization), PCR, real-time PCR,microarray analysis or sequencing.

The first sample can be obtained in a less intrusive or less invasivemethod than is the second sample. For example, the first sample can beurine or blood, and the second sample can be a biopsy. For example, thefirst sample can be a blood sample that is used to assess one or moreRNAs, and depending on the level of RNAs, a biopsy for histologicalexamination can be obtained to characterize the cancer, such as diagnosethe presence or absence of cancerous tissue or the stage of a cancer.

For example, if an RNA level in a first sample is between about 1500 toabout 9000 copies per microliter, such as at least about 1600, 1700,1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800, 2900,3000, 3100, 3200, 3300, 3400, 3500, 3600, 3700, 3800, 3900, 4000, 4100,4200, 4300, 4400, 4500, 4600, 4700, 4800, 4900, 5000, 5100, 5200, 5300,5400, 5500, 5600, 5700, 5800, 5900, 6000, 6100, 6200, 6300, 6400, 6500,6600, 6700, 6800, 6900, 7000, 7100, 7200, 7300, 7400, 7500, 7600, 7700,7800, 7900, 8000, 8100, 8200, 8300, 8400, 8500, 8600, 8700, 8800, or8900, a second sample, such as a biopsy or tissue sample forhistological examination is taken from the subject. In some embodiments,if the level is between about 1500 to about 4500 copies per microliter,a second sample is taken from the subject. In yet other embodiments, asecond sample is not obtained from a subject if the level of the RNA,such as a miRNA, is less than about 1500 copies per microliter, such asless than about 1100, 1200, 1300, 1400, or 1500.

In some embodiments, assessing one or more RNAs is used to determine theneed for a second or third sample, such as a second or third biopsy. Forexample, after an initial elevated serum miR-141 is observed followed bya negative biopsy or a negative second biopsy. Such method includes thesteps of obtaining a blood sample from a subject and determining anamount of miR-141 in serum of the subject's blood sample, and a biopsyis indicated when serum miR-141 is significantly different from amiR-141 amount in a control sample that corresponds to subjects withoutepithelial cancer, or to a previous determination of the same patient'smiR-141 levels, any significant increase in miR-141 level indicating theneed for another biopsy.

Sensitivity and Specificity

The methods and compositions disclosed herein can also provide increasedsensitivity and the specificity for characterizing cancers, such as fordetecting, diagnosing, prognosing, or monitoring for cancer recurrenceand therapeutic efficacy are provided herein. The sensitivity can bedetermined by: (number of true positives)/(number of truepositives+number of false negatives). The specificity can be determinedby: (number of true negatives)/(number of true negatives+number of falsepositives).

Assessing one or more RNAs disclosed herein can be used to characterizea cancer with at least about 70% or 75% specificity. For example, acancer can be characterized with greater than about 76, 77, 78, 79, 80,81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, or 97%specificity. The cancer can be characterized with at least about 97.1,97.2, 97.3, 97.4, 97.5, 97.6, 97.7, 97.8, 97.8, 97.9, 98.0, 98.1, 98.2,98.3, 98.4, 98.5, 98.6, 98.7, 98.8, 98.9, 99.0, 99.1, 998.2, 99.3, 99.4,99.5, 99.6, 99.7, 99.8, 99.9% specificity. In yet other embodiments, thecancer can be characterized with 100% specificity.

In some embodiments, the cancer can be characterized with at least about60% sensitivity, such as at least about 60, 65, 70, 75, 80, 81, 82, 83,84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, or 97% sensitivity.The cancer can be characterized with at least about 97.1, 97.2, 97.3,97.4, 97.5, 97.6, 97.7, 97.8, 97.8, 97.9, 98.0, 98.1, 98.2, 98.3, 98.4,98.5, 98.6, 98.7, 98.8, 98.9, 99.0, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6,99.7, 99.8, 99.9% sensitivity. In yet other embodiments, the cancer canbe characterized with 100% sensitivity.

In some embodiments, assessing a plurality of RNAs provides increasedspecificity or sensitivity in the characterization of cancer as comparedto assessing less than the plurality of RNAs. For example, thesensitivity or specificity may be at increased by at least about 5, 10,15, 20, 30, 35, 40, 50, 75, 100, 150, 200, 250, 500, 1000% or more thandetection with less than the plurality of RNAs. For example, thesensitivity for characterizing a cancer is 50% using one RNA, whereasusing an additional RNA provides an increased sensitivity of 60%, anincrease of 20%. Thus, in some embodiments, the number of RNAs analyzedis the number such that an increase in the number provides increasedsensitivity or specificity. In some embodiments, assessing at least 2,3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100,1000, 2500, 5000, 7500, 10,000, 100,000, 150,000, 200,000, 250,000,300,000, 350,000, 400,000, 450,000, 500,000, 750,000, or 1,000,000 RNAsprovide increased specificity or sensitivity in the characterization ofa cancer, as compared to less than the number of RNAs assessed. Forexample, assessing at least 2 RNAs, such as at least two miRNAs, canprovide increased specificity or sensitivity in the characterization ofcancer as compared to assessing one of the two miRNAs.

MicroRNAs

The one or more RNAs assessed herein can comprise one or more microRNAs(miRNAs, miRs). mRNAs are short RNA strands approximately 21-23nucleotides in length. mRNAs are encoded by genes that are transcribedfrom DNA but not translated into protein (non-coding RNA). Instead theyare processed from primary transcripts known as pri-miRNA to shortstem-loop structures called pre-miRNA and finally to functional miRNA,as the precursors typically form structures that fold back on each otherin self-complementary regions. They are then processed by the nucleaseDicer in animals or DCL1 in plants. Mature miRNA molecules are partiallycomplementary to one or more messenger RNA (mRNA) molecules. Thesequences of miRNA can be accessed at publicly available databases, suchas http://www.microRNA.org or http://www.mirz.unibas.ch/cgi/miRNA.cgi.

A number of miRNAs are involved in gene regulation, and miRNAs are partof a growing class of non-coding RNAs that is now recognized as a majortier of gene control. In some cases, miRNAs can interrupt translation bybinding to regulatory sites embedded in the 3′-UTRs of their targetmRNAs, leading to the repression of translation. Target recognitioninvolves complementary base pairing of the target site with the miRNA'sseed region (positions 2-8 at the miRNA's 5′ end), although the exactextent of seed complementarity is not precisely determined and can bemodified by 3′ pairing. In other cases, miRNAs function like smallinterfering RNAs (siRNA) and bind to perfectly complementary mRNAsequences to destroy the target transcript.

Characterization of a number of miRNAs indicates that they influence avariety of processes, including early development, cell proliferationand cell death, apoptosis and fat metabolism. For example, some miRNAs,such as lin-4, let-7, mir-14, mir-23, and bantam, have been shown toplay critical roles in cell differentiation and tissue development.Others are believed to have similarly important roles because of theirdifferential spatial and temporal expression patterns.

In some embodiments, a single miRNA is assessed to characterize acancer. In yet other embodiments, at least 2, 3, 4, 5, 6, 7, 8, 9, 10,15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, 1000, 2500, 5000, 7500,10,000, 100,000, 150,000, 200,000, 250,000, 300,000, 350,000, 400,000,450,000, 500,000, 750,000, or 1,000,000 miRNAs are assessed. In someembodiments, 1 or more miRNAs is assessed in combination with otherspecies of RNAs, such as mRNA, to characterize a cancer.

In some embodiments, the miRNAs are used to detect prostate cancer. Forexample, the level of a microRNA that is detectable in sample can beindicative of prostate cancer and levels that are not detectable are notindicative of prostate cancer. In some embodiments, detection of 1, 2,3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100,1000, 2500, 5000, 7500, 10,000, 100,000, 150,000, 200,000, 250,000,300,000, 350,000, 400,000, 450,000, 500,000, 750,000, 1,000,000 or moremiRNAs is used to detect prostate cancer. A change in the expressionlevel, such as absence, presence, underexpression or overexpression ofthe miRNA as compared to a reference level, such as a level determinedfor a subject without the cancer (such as age and sex controlled), canbe used to characterize a cancer for the subject.

For example, a reference level for classifying a prostate cancer asbenign or malignant can include obtaining a blood sample from a subject,determining an amount of a miRNA in the subject's blood sample, andcomparing the amount of the miRNA to one or more controls having benignprostate cancer or malignant prostate cancer. The step of comparing theamount of the miRNA to one or more controls may include the steps ofobtaining a range of the miRNA found in the blood for a plurality ofsubjects having benign prostate cancer to arrive at a first controlrange, obtaining a range of the miRNA found in the blood for a pluralityof subjects having malignant prostate cancer to arrive at a secondcontrol range, and comparing the amount of the miRNA in the subject'sblood sample with the first and second control ranges to determine ifthe subject's prostate cancer is classified as benign prostate cancer ormalignant prostate cancer.

MiR-200 Family

In some embodiments, the miRNA is a member of the miR-200 family. ThemiR-200 family is believed to determine the epithelial phenotype ofcancer cells by targeting the E-cadherin repressors ZEB1 and ZEB2. ThemiR-200 family includes miR-141, miR-236, miR-200a, mir-200b, mir-200cand mir-429. In some embodiments more than one miR-200 family member isanalyzed to detect an epithelial cancer.

For example, miR-141 can be obtained from blood (serum or plasma) andcorrelated with the occurrence of metatstatic epithelial cancer. MiR-141can be used to detect cancer recurrence and therapeutic efficacy forepithelial based cancers, such as prostate cancer, including the use ofmiR-141 to monitor subjects who have undergone surgical removal of theircancer. For example, currently subjects are monitored with other markerslike serum PSA for prostate cancer. A steady rise in serum PSA wouldindicate a recurrence and spread of the cancer. However, many prostatecancer metastases do not express PSA and are therefore missed by thismonitoring method. By the time the cancer has been detected it has oftenspread beyond any treatment options. Other epithelial cancers havesimilar issues regarding current diagnostic regimens.

Gene Associated mRNAs

The miRNA can also be a miRNA that interacts with the mRNA of PFKFB3,RHAMM (HMMR), cDNA FLJ42103, ASPM, CENPF, NCAPG, Androgen Receptor,EGFR, HSP90, SPARC, DNMT3B, GART, MGMT, SSTR3, or TOP2B. For example,such as the microRNAs that can be detected, and the gene with which theyare associated as listed in Table 1. The miR5 can be used tocharacterize an epithelial cancer, such as prostate cancer.

TABLE 1 Gene Name and Their Associated miRNAs Gene miRNA Associated withGene Androgen receptor hsa-miR-124a hsa-miR-130a hsa-miR-130bhsa-miR-143 hsa-miR-149 hsa-miR-194 hsa-miR-29b hsa-miR-29c hsa-miR-301hsa-miR-30a-5p hsa-miR-30d hsa-miR-30e-5p hsa-miR-337 hsa-miR-342hsa-miR-368 hsa-miR-488 hsa-miR-493-5p hsa-miR-506 hsa-miR-512-5phsa-miR-644 hsa-miR-768-5p hsa-miR-801 DNMT3B hsa-miR-618 hsa-miR-1253hsa-miR-765 hsa-miR-561 hsa-miR-330-5p hsa-miR-326 hsa-miR-188hsa-miR-203 hsa-miR-221 hsa-miR-222 hsa-miR-26a hsa-miR-26b hsa-miR-29ahsa-miR-29a hsa-miR-29b hsa-miR-29c hsa-miR-370 hsa-miR-379 hsa-miR-429hsa-miR-519e* hsa-miR-598 hsa-miR-618 hsa-miR-635 GART hsa-miR-101hsa-miR-101 hsa-miR-141 hsa-miR-144 hsa-miR-182 hsa-miR-189 hsa-miR-199ahsa-miR-199b hsa-miR-200a hsa-miR-200b hsa-miR-202 hsa-miR-203hsa-miR-223 hsa-miR-329 hsa-miR-383 hsa-miR-429 hsa-miR-433hsa-miR-485-5p hsa-miR-493-5p hsa-miR-499 hsa-miR-519a hsa-miR-519bhsa-miR-519c hsa-miR-569 hsa-miR-591 hsa-miR-607 hsa-miR-627 hsa-miR-635hsa-miR-659 MGMT hsa-miR-122a hsa-miR-142-3p hsa-miR-17-3p hsa-miR-181ahsa-miR-181b hsa-miR-181c hsa-miR-181d hsa-miR-199b hsa-miR-200a*hsa-miR-217 hsa-miR-302b* hsa-miR-32 hsa-miR-324-3p hsa-miR-34ahsa-miR-371 hsa-miR-425-5p hsa-miR-496 hsa-miR-514 hsa-miR-515-3phsa-miR-516-3p hsa-miR-574 hsa-miR-597 hsa-miR-603 hsa-miR-653hsa-miR-655 hsa-miR-92 hsa-miR-92b hsa-miR-99a Top2B hsa-miR-548fhsa-miR-548a-3p hsa-miR-548g hsa-miR-513a-3p hsa-miR-548c-3p hsa-miR-101hsa-miR-653 hsa-miR-548d-3p hsa-miR-575 hsa-miR-297 hsa-miR-576-3phsa-miR-548b-3p hsa-miR-624 hsa-miR-548n hsa-miR-758 hsa-miR-1253hsa-miR-1324 hsa-miR-23b hsa-miR-320a hsa-miR-320b hsa-miR-1183hsa-miR-1244 hsa-miR-23a hsa-miR-451 hsa-miR-568 hsa-miR-1276hsa-miR-548e hsa-miR-590-3p hsa-miR-1 hsa-miR-101 hsa-miR-126hsa-miR-126* hsa-miR-129 hsa-miR-136 hsa-miR-140 hsa-miR-141 hsa-miR-144hsa-miR-147 hsa-miR-149 hsa-miR-18 hsa-miR-181b hsa-miR-181c hsa-miR-182hsa-miR-184 hsa-miR-186 hsa-miR-189 hsa-miR-191 hsa-miR-19a hsa-miR-19bhsa-miR-200a hsa-miR-206 hsa-miR-210 hsa-miR-218 hsa-miR-223 hsa-miR-23ahsa-miR-23b hsa-miR-24 hsa-miR-27a hsa-miR-302 hsa-miR-30a hsa-miR-31hsa-miR-320 hsa-miR-323 hsa-miR-362 hsa-miR-374 hsa-miR-383hsa-miR-409-3p hsa-miR-451 hsa-miR-489 hsa-miR-493-3p hsa-miR-514hsa-miR-542-3p hsa-miR-544 hsa-miR-548a hsa-miR-548b hsa-miR-548chsa-miR-548d hsa-miR-559 hsa-miR-568 hsa-miR-575 hsa-miR-579 hsa-miR-585hsa-miR-591 hsa-miR-598 hsa-miR-613 hsa-miR-649 hsa-miR-651 hsa-miR-758hsa-miR-768-3p hsa-miR-9* HSP90 hsa-miR-1 hsa-miR-513a-3phsa-miR-548d-3p hsa-miR-642 hsa-miR-206 hsa-miR-450b-3p hsa-miR-152hsa-miR-148a hsa-miR-148b hsa-miR-188-3p hsa-miR-23a hsa-miR-23bhsa-miR-578 hsa-miR-653 hsa-miR-1206 hsa-miR-192 hsa-miR-215hsa-miR-181b hsa-miR-181d hsa-miR-223 hsa-miR-613 hsa-miR-769-3phsa-miR-99a hsa-miR-100 hsa-miR-454 hsa-miR-548n hsa-miR-640 hsa-miR-99bhsa-miR-150 hsa-miR-181a hsa-miR-181c hsa-miR-522 hsa-miR-624 hsa-miR-1hsa-miR-130a hsa-miR-130b hsa-miR-146 hsa-miR-148a hsa-miR-148bhsa-miR-152 hsa-miR-181a hsa-miR-181b hsa-miR-181c hsa-miR-204hsa-miR-206 hsa-miR-211 hsa-miR-212 hsa-miR-215 hsa-miR-223 hsa-miR-23ahsa-miR-23b hsa-miR-301 hsa-miR-31 hsa-miR-325 hsa-miR-363* hsa-miR-566hsa-miR-9 hsa-miR-99b ASPM hsa-miR-1 hsa-miR-122a hsa-miR-135ahsa-miR-135b hsa-miR-137 hsa-miR-153 hsa-miR-190 hsa-miR-206 hsa-miR-320hsa-miR-380-3p hsa-miR-382 hsa-miR-433 hsa-miR-453 hsa-miR-493-5phsa-miR-496 hsa-miR-499 hsa-miR-507 hsa-miR-517b hsa-miR-548ahsa-miR-548c hsa-miR-567 hsa-miR-568 hsa-miR-580 hsa-miR-602 hsa-miR-651hsa-miR-653 hsa-miR-758 hsa-miR-9* SPARC hsa-miR-768-5p hsa-miR-203hsa-miR-196a hsa-miR-569 hsa-miR-187 hsa-miR-641 hsa-miR-1275hsa-miR-432 hsa-miR-622 hsa-miR-296-3p hsa-miR-646 hsa-miR-196bhsa-miR-499-5p hsa-miR-590-5p hsa-miR-495 hsa-miR-625 hsa-miR-1244hsa-miR-512-5p hsa-miR-1206 hsa-miR-1303 hsa-miR-186 hsa-miR-302dhsa-miR-494 hsa-miR-562 hsa-miR-573 hsa-miR-10a hsa-miR-203 hsa-miR-204hsa-miR-211 hsa-miR-29a hsa-miR-29b hsa-miR-29c hsa-miR-29c hsa-miR-339hsa-miR-433 hsa-miR-452 hsa-miR-515-5p hsa-miR-517a hsa-miR-517bhsa-miR-517c hsa-miR-592 hsa-miR-96 PFKB3 hsa-miR-513a-3p hsa-miR-1286hsa-miR-488 hsa-miR-539 hsa-miR-658 hsa-miR-524-5p hsa-miR-1258hsa-miR-150 hsa-miR-216b hsa-miR-377 hsa-miR-135a hsa-miR-26ahsa-miR-548a-5p hsa-miR-26b hsa-miR-520d-5p hsa-miR-224 hsa-miR-1297hsa-miR-1197 hsa-miR-182 hsa-miR-452 hsa-miR-509-3-5p hsa-miR-548mhsa-miR-625 hsa-miR-509-5p hsa-miR-1266 hsa-miR-135b hsa-miR-190bhsa-miR-496 hsa-miR-616 hsa-miR-621 hsa-miR-650 hsa-miR-105 hsa-miR-19ahsa-miR-346 hsa-miR-620 hsa-miR-637 hsa-miR-651 hsa-miR-1283hsa-miR-590-3p hsa-miR-942 hsa-miR-1185 hsa-miR-577 hsa-miR-602hsa-miR-1305 hsa-miR-220c hsa-miR-1270 hsa-miR-1282 hsa-miR-432hsa-miR-491-5p hsa-miR-548n hsa-miR-765 hsa-miR-768-3p hsa-miR-924 HMMRhsa-miR-936 hsa-miR-656 hsa-miR-105 hsa-miR-361-5p hsa-miR-194hsa-miR-374a hsa-miR-590-3p hsa-miR-186 hsa-miR-769-5p hsa-miR-892ahsa-miR-380 hsa-miR-875-3p hsa-miR-208a hsa-miR-208b hsa-miR-586hsa-miR-125a-3p hsa-miR-630 hsa-miR-374b hsa-miR-411 hsa-miR-629hsa-miR-1286 hsa-miR-1185 hsa-miR-16 hsa-miR-200b hsa-miR-671-5phsa-miR-95 hsa-miR-421 hsa-miR-496 hsa-miR-633 hsa-miR-1243hsa-miR-127-5p hsa-miR-143 hsa-miR-15b hsa-miR-200c hsa-miR-24hsa-miR-34c-3p CENPF hsa-miR-30c hsa-miR-30b hsa-miR-190 hsa-miR-508-3phsa-miR-384 hsa-miR-512-5p hsa-miR-548p hsa-miR-297 hsa-miR-520fhsa-miR-376a hsa-miR-1184 hsa-miR-577 hsa-miR-708 hsa-miR-205hsa-miR-376b hsa-miR-520g hsa-miR-520h hsa-miR-519d hsa-miR-596hsa-miR-768-3p hsa-miR-340 hsa-miR-620 hsa-miR-539 hsa-miR-567hsa-miR-671-5p hsa-miR-1183 hsa-miR-129-3p hsa-miR-636 hsa-miR-106ahsa-miR-1301 hsa-miR-17 hsa-miR-20a hsa-miR-570 hsa-miR-656 hsa-miR-1263hsa-miR-1324 hsa-miR-142-5p hsa-miR-28-5p hsa-miR-302b hsa-miR-452hsa-miR-520d-3p hsa-miR-548o hsa-miR-892b hsa-miR-302d hsa-miR-875-3phsa-miR-106b hsa-miR-1266 hsa-miR-1323 hsa-miR-20b hsa-miR-221hsa-miR-520e hsa-miR-664 hsa-miR-920 hsa-miR-922 hsa-miR-93 hsa-miR-1228hsa-miR-1271 hsa-miR-30e hsa-miR-483-3p hsa-miR-509-3-5p hsa-miR-515-3phsa-miR-519e hsa-miR-520b hsa-miR-520c-3p hsa-miR-582-3p NCAPG2hsa-miR-876-5p hsa-miR-1260 hsa-miR-1246 hsa-miR-548c-3p hsa-miR-1224-3phsa-miR-619 hsa-miR-605 hsa-miR-490-5p hsa-miR-186 hsa-miR-448hsa-miR-129-5p hsa-miR-188-3p hsa-miR-516b hsa-miR-342-3p hsa-miR-1270hsa-miR-548k hsa-miR-654-3p hsa-miR-1290 hsa-miR-656 hsa-miR-34bhsa-miR-520g hsa-miR-1231 hsa-miR-1289 hsa-miR-1229 hsa-miR-23ahsa-miR-23b hsa-miR-616 hsa-miR-620 EGFR hsa-miR-105 hsa-miR-128ahsa-miR-128b hsa-miR-140 hsa-miR-141 hsa-miR-146a hsa-miR-146bhsa-miR-27a hsa-miR-27b hsa-miR-302a hsa-miR-302d hsa-miR-370hsa-miR-548c hsa-miR-574 hsa-miR-587 hsa-miR-7 SSTR3 hsa-miR-125ahsa-miR-125b hsa-miR-133a hsa-miR-133b hsa-miR-136 hsa-miR-150hsa-miR-21 hsa-miR-380-5p hsa-miR-504 hsa-miR-550 hsa-miR-671hsa-miR-766 hsa-miR-767-3p

Therefore, if one or more of the miRNAs in Table 1 appear in aconcentration greater than 9000 copies per microliter of sample, such asa serum sample, the subject can be diagnosed with benign prostatecancer. If one or more of the miRNAs in Table 1 appear in aconcentration less than 3000 copies per microliter of sample, thesubject can be diagnosed with malignant prostate cancer. In someembodiments, if one or more of the miRNAs in Table 1 appear in aconcentration between about 1000 to about 4500 copies per microliter ofsample from a subject, a second biological sample from the subject isobtained. The second sample can analyzed by histochemical analysis, suchas by immunohistochemistry.

Furthermore, in various embodiments the micro RNAs associated with thegenes for use in the methods and compositions of the invention (e.g.,those overexpressed in prostate cancer) can be found in the micro RNAdatabase online at www.microrna.org: or microrna.sanger.ac.uk/sequences,or the predicted miRNAs queried athttp://www.diana.pcbi.upenn.edu/cgi-bin/miRGen/v3/.

The miRNA that interacts with PFKFB3 can be miR-513a-3p, miR-128,miR-488, miR-539, miR-658, miR-524-5p, miR-1258, miR-150, miR-216b,miR-377, miR-135a, miR-26a, miR-548a-5p, miR-26b, miR-520d-5p, miR-224,miR-1297, miR-1197, miR-182, miR-452, miR-509-3-5p, miR-548m, miR-625,miR-509-5p, miR-1266, miR-135b, miR-190b, miR-496, miR-616, miR-621,miR-650, miR-105, miR-19a, miR-346, miR-620, miR-637, miR-651, miR-1283,miR-590-3p; miR-942, miR-1185, miR-577, miR-602, miR-1305, miR-220c,miR-1270, miR-1282, miR-432, miR-491-5p, miR-548n, miR-765, miR-768-3por miR-924. The one or more miRNA that interacts with PFKFB3 can bedetected in a sample from a subject, such as determining the copy numberper microliter of the one or more miRNA, and used to characterize acancer. The copy number per microliter of miRNA can also be used todetermine whether a second biological sample from a subject should beobtained for further analysis, such as by a pathologist.

The miRNA that interacts with RHAMM can be miR-936, miR-656, miR-105,miR-361-5p, miR-194, miR-374a, miR-590-3p, miR-186, miR-769-5p,miR-892a, miR-380, miR-875-3p, miR-208a, miR-208b, miR-586, miR-125a-3p,miR-630, miR-374b, miR-411, miR-629, miR-1286, miR-1185, miR-16,miR-200b, miR-671-5p, miR-95, miR-421, miR-496, miR-633, miR-1243,miR-127-5p, miR-143, miR-15b, miR-200c, miR-24 or miR-34c-3p. The one ormore miRNA that interacts with RHAMM can be detected in a sample from asubject, such as determining the copy number per microliter of the oneor more miRNA, and used to characterize a cancer. The copy number permicroliter of miRNA can also be used to determine whether a secondbiological sample from a subject should be obtained for furtheranalysis, such as by a pathologist.

The miRNA that interacts with CENPF can be miR-30c, miR-30b, miR-190,miR-508-3p, miR-384, miR-512-5p, miR-548p, miR-297, miR-520f, miR-376a,miR-1184, miR-577, miR-708, miR-205, miR-376b, miR-520g, miR-520h,miR-519d, miR-596, miR-768-3p, miR-340, miR-620, miR-539, miR-567,miR-671-5p, miR-1183, miR-129-3p, miR-636, miR-106a, miR-1301, miR-17,miR-20a, miR-570, miR-656, miR-1263, miR-1324, miR-142-5p, miR-28-5p,miR-302b, miR-452, miR-520d-3p, miR-548o, miR-892b, miR-302d,miR-875-3p, miR-106b, miR-1266, miR-1323, miR-20b, miR-221, miR-520e,miR-664, miR-920, miR-922, miR-93, miR-1228, miR-1271, miR-30e,miR-483-3p, miR-509-3-5p, miR-515-3p, miR-519e, miR-520h, miR-520c-3p ormiR-582-3p. The one or more miRNA that interacts with CENPF can bedetected in a sample from a subject, such as determining the copy numberper microliter of the one or more miRNA, and used to characterize acancer. The copy number per microliter of miRNA can also be used todetermine whether a second biological sample from a subject should beobtained for further analysis, such as by a pathologist.

The miRNA that interacts with NCAPG can be miR-876-5p, miR-1260,miR-1246, miR-548c-3p, miR-1224-3p, miR-619, miR-605, miR-490-5p,miR-186, miR-448, miR-129-5p, miR-188-3p, miR-516b, miR-342-3p,miR-1270, miR-548k, miR-654-3p, miR-1290, miR-656, miR-34b, miR-520g,miR-1231, miR-1289, miR-1229, miR-23a, miR-23b, miR-616 or miR-620. Theone or more miRNA that interacts with NCAPG can be detected in a samplefrom a subject, such as determining the copy number per microliter ofthe one or more miRNA, and used to characterize a cancer. The copynumber per microliter of miRNA can also be used to determine whether asecond biological sample from a subject should be obtained for furtheranalysis, such as by a pathologist.

The miRNA that interacts with Androgen Receptor can be miR-124a,miR-130a, miR-130h, miR-143, miR-149, miR-194, miR-29h, miR-29c,miR-301, miR-30a-5p, miR-30d, miR-30e-5p, miR-337, miR-342, miR-368,miR-488, miR-493-5p, miR-506, miR-512-5p, miR-644, miR-768-5p ormiR-801. The one or more miRNA that interacts with Androgen Receptor canbe detected in a sample from a subject, such as determining the copynumber per microliter of the one or more miRNA, and used to characterizea cancer. The copy number per microliter of miRNA can also be used todetermine whether a second biological sample from a subject should beobtained for further analysis, such as by a pathologist.

The miRNA that interacts with EGFR can be miR-105, miR-128a, miR-128b,miR-140, miR-141, miR-146a, miR-146b, miR-27a, miR-27b, miR-302a,miR-302d, miR-370, miR-548c, miR-574, miR-587 or miR-7. The one or moremiRNA that interacts with EGFR can be detected in a sample from asubject, such as determining the copy number per microliter of the oneor more miRNA, and used to characterize a cancer. The copy number permicroliter of miRNA can also be used to determine whether a secondbiological sample from a subject should be obtained for furtheranalysis, such as by a pathologist.

The miRNA that interacts with HSP90 can be miR-1, miR-513a-3p,miR-548d-3p, miR-642, miR-206, miR-450b-3p, miR-152, miR-148a, miR-148b,miR-188-3p, miR-23a, miR-23b, miR-578, miR-653, miR-1206, miR-192,miR-215, miR-181b, miR-181d, miR-223, miR-613, miR-769-3p, miR-99a,miR-100, miR-454, miR-548n, miR-640, miR-99b, miR-150, miR-181a,miR-181c, miR-522, miR-624, miR-130a, miR-130b, miR-146, miR-148a,miR-148b, miR-152, miR-181a, miR-181b, miR-181c, miR-204, miR-206,miR-211, miR-212, miR-215, miR-223, miR-23a, miR-23b, miR-301, miR-31,miR-325, miR-363, miR-566, miR-9 or miR-99h. The one or more miRNA thatinteracts with HSP90 can be detected in a sample from a subject, such asdetermining the copy number per microliter of the one or more miRNA, andused to characterize a cancer. The copy number per microliter of miRNAcan also be used to determine whether a second biological sample from asubject should be obtained for further analysis, such as by apathologist.

The miRNA that interacts with SPARC can be miR-768-5p, miR-203,miR-196a, miR-569, miR-187, miR-641, miR-1275, miR-432, miR-622,miR-296-3p, miR-646, miR-196b, miR-499-5p, miR-590-5p, miR-495, miR-625,miR-1244, miR-512-5p, miR-1206, miR-1303, miR-186, miR-302d, miR-494,miR-562, miR-573, miR-10a, miR-203, miR-204, miR-211, miR-29, miR-29b,miR-29c, miR-339, miR-433, miR-452, miR-515-5p, miR-517a, miR-517b,miR-517c, miR-592 or miR-96. The one or more miRNA that interacts withSPARC can be detected in a sample from a subject, such as determiningthe copy number per microliter of the one or more miRNA, and used tocharacterize a cancer. The copy number per microliter of miRNA can alsobe used to determine whether a second biological sample from a subjectshould be obtained for further analysis, such as by a pathologist.

The miRNA that interacts with DNMT3B can be miR-618, miR-1253, miR-765,miR-561, miR-330-5p, miR-326, miR-188, miR-203, miR-221, miR-222,miR-26a, miR-26b, miR-29a, miR-29b, miR-29c, miR-370, miR-379, miR-429,miR-519e, miR-598, miR-618 or miR-635. The one or more miRNA thatinteracts with DNMT3B can be detected in a sample from a subject, suchas determining the copy number per microliter of the one or more miRNA,and used to characterize a cancer. The copy number per microliter ofmiRNA can also be used to determine whether a second biological samplefrom a subject should be obtained for further analysis, such as by apathologist.

The miRNA that interacts with GART can be miR-101, miR-141, miR-144,miR-182, miR-189, miR-199a, miR-199h, miR-200a, miR-200b, miR-202,miR-203, miR-223, miR-329, miR-383, miR-429, miR-433, miR-485-5p,miR-493-5p, miR-499, miR-519a, miR-519b, miR-519c, miR-569, miR-591,miR-607, miR-627, miR-635, miR-636 or miR-659. The one or more miRNAthat interacts with GART can be detected in a sample from a subject,such as determining the copy number per microliter of the one or moremiRNA, and used to characterize a cancer. The copy number per microliterof miRNA can also be used to determine whether a second biologicalsample from a subject should be obtained for further analysis, such asby a pathologist.

The miRNA that interacts with MGMT can be miR-122a, miR-142-3p,miR-17-3p, miR-181a, miR-181b, miR-181c, miR-181d, miR-199b, miR-200a,miR-217, miR-302b, miR-32, miR-324-3p, miR-34a, miR-371, miR-425-5p,miR-496, miR-514, miR-515-3p, miR-516-3p, miR-574, miR-597, miR-603,miR-653, miR-655, miR-92, miR-92h or miR-99a. The one or more miRNA thatinteracts with MGMT can be detected in a sample from a subject, such asdetermining the copy number per microliter of the one or more miRNA, andused to characterize a cancer. The copy number per microliter of miRNAcan also be used to determine whether a second biological sample from asubject should be obtained for further analysis, such as by apathologist.

The miRNA that interacts with SSTR3 can be miR-125a, miR-125b, miR-133a,miR-133b, miR-136, miR-150, miR-21, miR-380-5p, miR-504, miR-550,miR-671, miR-766 or miR-767-3p. The one or more miRNA that interactswith SSTR3 can be detected in a sample from a subject, such asdetermining the copy number per microliter of the one or more miRNA, andused to characterize a cancer. The copy number per microliter of miRNAcan also be used to determine whether a second biological sample from asubject should be obtained for further analysis, such as by apathologist.

The miRNA that interacts with TOP2B can be miR-548f, miR-548a-3p,miR-548g, miR-513a-3p, miR-548c-3p, miR-101, miR-653, miR-548d-3p,miR-575, miR-297, miR-576-3p, miR-548h-3p, miR-624, miR-548n, miR-758,miR-1253, miR-1324, miR-23b, miR-320a, miR-320b, miR-1183, miR-1244,miR-23a, miR-451, miR-568, miR-1276, miR-548e, miR-590-3p, miR-1,miR-101, miR-126, miR-129, miR-136, miR-140, miR-141, miR-144, miR-147,miR-149, miR-18, miR-181b, miR-181c, miR-182, miR-184, miR-186, miR-189,miR-191, miR-19a, miR-19b, miR-200a, miR-206, miR-210, miR-218, miR-223,miR-23a, miR-23b, miR-24, miR-27a, miR-302, miR-30a, miR-31, miR-320,miR-323, miR-374, miR-383, miR-409-3p, miR-451, miR-493-3p, miR-514,miR-542-3p, miR-544, miR-548a, miR-548b, miR-548c, miR-548d, miR-559,miR-568, miR-575, miR-579, miR-585, miR-591, miR-598, miR-613, miR-649,miR-651, miR-758, miR-768-3p or miR-9. The one or more miRNA thatinteracts with TOP2B can be detected in a sample from a subject, such asdetermining the copy number per microliter of the one or more miRNA, andused to characterize a cancer. The copy number per microliter of miRNAcan also be used to determine whether a second biological sample from asubject should be obtained for further analysis, such as by apathologist.

In some embodiments, the one or more miRNA is selected from the groupconsisting of miR-498, miR-503miR-198, miR-302c, miR-345, miR-491-5p,miR-513, miR-26a-1/2, miR-375, miR-425, miR-194-1/2, miR-181a-112,let-71, miR-25, miR-449, and miR-92-1/2. The one or more miRNAs can alsobe selected from the group consisting of: let-7a, let-7b, let-7c,let-7d, let-7g, miR-145, miR-195, miR-199, miR-497, let-7f, miR-22,miR-30_(—)5p, miR-490, miR-133a-1, miR-1-2, miR-218-2, miR-345, miR-410,miR-7-1/2, miR-145, miR-34a, miR-487, or let-7b. In other embodiments,the one or more miRNA is miR-99, miR-101, miR-130, miR-135, miR-141,miR-148, miR-182, miR-186, miR-206, miR-320, miR-374, miR-433, miR-496,miR-517, miR-590, miR-620, miR-768, miR-223, miR-203, miR-199, miR-519,miR-302, miR-30, miR-20, miR-200, miR-23, miR-29, miR-181, miR-548, andmiR-370. The one or more miRNAs can be detected in a sample from asubject, such as determining the copy number per microliter of the oneor more miRNA, and used to characterize a cancer. The copy number permicroliter of miRNA can also be used to determine whether a secondbiological sample from a subject should be obtained for furtheranalysis, such as by a pathologist.

In another embodiment, the one or more miRNA is miR-629, miR-671-3p,miR-9, miR-491, miR-182, miR125a—3p, miR-324-5p, miR-148b, miR-222,miR-141 or miR-370. The one or more miRNAs selected from the groupconsisting of miR-629, miR-671-3p, miR-9, miR-491, miR-182, miR125a-3p,miR-324-5p, miR-148b, miR-222, and miR-141 can be used to characterizeprostate cancer.

Furthermore, one or more miRNAs, such as those described in Table 1, canform a RNA patter with the mRNA of AR, PCA3, or any combination thereof,and used to characterize a cancer, such as prostate cancer. The RNApattern can also comprise the snoRNA U50.

Assessing RNA

Assessing the RNA may be qualitative or quantitative. Assessing RNAincludes detecting the RNA, such as determining the expression level(such as overexpression or underexpression as compared to a control, thepresence or absence of an RNA), determining the sequence of the RNA,determining any modifications of the RNA, or detecting any mutations orvariations of the RNA. The RNA level may be determined to be present orabsent, greater than or less than a control, or given a numerical valuefor the amount of RNA, such as the copies of RNA per microliter. Theexpression level of an RNA can be quantified, by absolute or relativequantification. Absolute quantification may be accomplished by inclusionof known concentration(s) of one or more target nucleic acids andreferencing the hybridization intensity of unknowns with the knowntarget nucleic acids (e.g. through generation of a standard curve).Alternatively, relative quantification can be accomplished by comparisonof hybridization signals between two or more genes, or between two ormore treatments to quantify the changes in hybridization intensity and,by implication, transcription level.

The RNA for assessment can be is isolated from a biological sample. TheRNA can be isolated from exosomes of a biological sample, such asisolated exosomes using methods as described above.

The RNA can be isolated using kits for performing membrane based RNApurification, which are commercially available. Generally, kits areavailable for the small-scale (30 mg or less) preparation of RNA fromcells and tissues (e.g. QIAGEN RNeasy Mini kit), for the medium scale(250 mg tissue) (e.g. QIAGEN RNeasy Midi kit), and for the large scale(1 g maximum) (QIAGEN RNeasy Maxi kit). Alternatively, RNA can beisolated using the method described in U.S. Pat. No. 7,267,950, or U.S.Pat. No. 7,267,950.

The RNA or nucleic acids derived from the RNA can be used for analysis.As used herein, a nucleic acid derived from an RNA refers to a nucleicacid for whose synthesis the RNA, a mRNA transcript, or a subsequencethereof has ultimately served as a template. Thus, a cDNA reversetranscribed from a transcript, an RNA transcribed from that cDNA, a DNAamplified from the cDNA, an RNA transcribed from the amplified DNA, andthe like are all derived from the transcript and detection of suchderived products is indicative of the presence and/or abundance of theoriginal transcript in a sample. Thus, suitable samples include, but arenot limited to, transcripts of the gene or genes, cDNA reversetranscribed from the transcript, cRNA transcribed from the cDNA, DNAamplified from the genes, RNA transcribed from amplified DNA, and thelike.

The RNA can be detected by detecting one or more labels attached to thesample RNA. The labels may be incorporated by any of a number of meanswell known to those of skill in the art. Detectable labels suitable foruse in the present invention include any composition detectable byspectroscopic, photochemical, biochemical, immunochemical, electrical,optical or chemical means. Useful labels in the present inventioninclude biotin for staining with labeled streptavidin conjugate,magnetic beads (e.g., Dynabeads™), fluorescent dyes (e.g., fluorescein,texas red; rhodamine, green fluorescent protein, and the like),radiolabels (e.g., 3H, 125I, 35S, 14C, or 32P), enzymes (e.g., horseradish peroxidase, alkaline phosphatase and others commonly used in anELISA), and colorimetric labels such as colloidal gold or colored glassor plastic (e.g., polystyrene, polypropylene, latex, etc.) heads. Meansof detecting such labels are well known to those of skill in the art.Thus, for example, radiolabels may be detected using photographic filmor scintillation counters, fluorescent markers may be detected using aphotodetector to detect emitted light. Enzymatic labels are typicallydetected by providing the enzyme with a substrate and detecting thereaction product produced by the action of the enzyme on the substrate,and colorimetric labels are detected by simply visualizing the coloredlabel. For example, miRNAs can be labeled and detect, such as using aradioactive phosphate at the 5′ end of the miRNA population can be usedby using a polynucleotide kinase (Krichevsky A M, King K S, Donahue C P,Khrapko K, Kosik K S (2003) RNA 9: 1274-1281) or a radiolabeled, singlenucleotide at the 3′ end using RNA ligase (see for example, U.S. Pat.No. 7,541,144). Commercially available kits can also be used to labelthe RNA. For example, miRNA can be labeled using kits from Ambion (e.g.mirVana™ labeling kit), Exiqon (e.g. miRCURY LNA microRNA ArrayHy3™/Hy5™ Power Labeling kit), Integrated DNA Technologies (e.g. miRNAStarFire Nucleic Acid Labling) Mirus Bio Corporation (e.g. LabelIT miRNALabeling Kit) and others.

In one embodiment, after RNA has been isolated, to detect the RNA ofinterest, cDNA can be synthesized and either Taqman assays for specificmRNA targets can be performed according to manufacturer's protocol, oran expression microarray can be performed to look at highly multiplexedsets of expression markers in one experiment. Methods for establishinggene expression profiles include determining the amount of RNA that isproduced by a gene that can code for a protein or peptide. This can beaccomplished by reverse transcriptase PCR (RT-PCR), competitive RT-PCR,real time RT-PCR, differential display RT-PCR, quantitative RT-PCR,Northern Blot analysis and other related tests. These techniques can beperformed using individual PCR reactions.

In some embodiments, complimentary DNA (cDNA) or complimentary RNA(cRNA) produced from mRNA is analyzed via microarray. The level of amiRNA gene product in a sample can be measured using any technique thatis suitable for assessing RNA expression levels in a biological sample,including but not limited to Northern blot analysis, RT-PCR, in situhybridization or microarray analysis. RNA detection can also be byhybridization with allele-specific probes, enzymatic mutation detection,ligation chain reaction (LCR), oligonucleotide ligation assay (OLA),flow-cytometric heteroduplex analysis, chemical cleavage of mismatches,mass spectrometry, nucleic acid sequencing, single strand conformationpolymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE),temperature gradient gel electrophoresis (TGGE), restriction fragmentpolymorphisms, serial analysis of gene expression (SAGE), or anycombinations thereof.

If a quantitative result is desired, the methods disclosed hereintypically use one or more controls for the relative frequencies of theamplified nucleic acids to achieve quantitative amplification. Methodsof quantitative amplification are well known to those of skill in theart. For example, quantitative PCR involves simultaneously co-amplifyinga known quantity of a control sequence using the same primers. Thisprovides an internal standard that may be used to calibrate the PCRreaction. Other suitable amplification methods include, but are notlimited to polymerase chain reaction (PCR) Innis, et al., PCR Protocols,A guide to Methods and Application. Academic Press, Inc. San Diego,(1990)), ligase chain reaction (LCR) (see Wu and Wallace, Genomics, 4:560 (1989). Landegren, et al., Science. 241: 1077 (1988) and Barringer,et al., Gene, 89: 117 (1990)), transcription amplification (Kwoh, etal., Proc. Natl. Acad. Sci. USA, 86: 1173 (1989)), and self-sustainedsequence replication (Guatelli, et al., Proc. Nat. Acad. Sci. USA,87:1874 (1990)). Additional nucleic acid quantification methods known inthe art include RT-PCR, Christmas-tree, ligase chain reaction, massspectrometry, TMA, NASBA, branched chain reaction, and reversetranscriptase ligase chain reaction.

Additional detection and/or measurement methods include nucleic acidhybridization. Nucleic acid hybridization simply involves contacting aprobe and target nucleic acid under conditions where the probe and itscomplementary target can form stable hybrid duplexes throughcomplementary base pairing. As used herein, hybridization conditionsrefer to standard hybridization conditions under which nucleic acidmolecules are used to identify similar nucleic acid molecules. Suchstandard conditions are disclosed, for example, in Sambrook et al.,Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Labs Press,1989. Sambrook et al., ibid., is incorporated by reference herein in itsentirety (see specifically, pages 9.31-9.62). In addition, formulae tocalculate the appropriate hybridization and wash conditions to achievehybridization permitting varying degrees of mismatch of nucleotides aredisclosed, for example, in Meinkoth et al., 1984, Anal. Biochem. 138,267-284; Meinkoth et al., ibid., is incorporated by reference herein inits entirety. Nucleic acids that do not form hybrid duplexes are washedaway from the hybridized nucleic acids and the hybridized nucleic acidscan then be detected, typically through detection of an attacheddetectable label. It is generally recognized that nucleic acids aredenatured by increasing the temperature or decreasing the saltconcentration of the buffer containing the nucleic acids. Under lowstringency conditions (e.g., low temperature and/or high salt) hybridduplexes (e.g., DNA:DNA, RNA:RNA, or RNA:DNA) will form even where theannealed sequences are not perfectly complementary. Thus specificity ofhybridization is reduced at lower stringency. Conversely, at higherstringency (e.g., higher temperature or lower salt) successfulhybridization requires fewer mismatches.

Nucleic acid arrays can be used to detect the one or more RNAs of asample. The production and application of high-density arrays in geneexpression monitoring have been disclosed previously in, for example, WO97/10365; WO 92/10588; WO95/35505; U.S. Pat. Nos. 6,040,138; 5,445,934;5,532,128; 5,556,752; 5,242,974; 5,384,261; 5,405,783; 5,412,087;5,424,186; 5,429,807; 5,436,327; 5,472,672; 5,527,681; 5,529,756;5,545,531; 5,554,501; 5,561,071; 5,571,639; 5,593,839; 5,599,695;5,624,711; 5,658,734; and 5,700,637; and Hacia et al. (1996) NatureGenetics 14:441-447; Lockhart et al. (1996) Nature Biotechnol.14:1675-1680; and De Risi et al. (1996) Nature Genetics 14:457-460.

In general, in an array, an oligonucleotide, or a cDNA, genomic DNA, orfragment thereof, of a known sequence occupies a known location on asubstrate. A nucleic acid sample is hybridized with an array and theamount of nucleic acids hybridized to each probe in the array isquantified. One quantifying method is to use confocal microscope andfluorescent labels. Commercially available array platform systems, suchas from Affymetrix (Santa Clara, Calif.), Agilent (Santa Clara, Calif.),Atlas™ (Clontech, Mountain View, Calif.), Exiqon (Denmark) and otherscan be used. One can use the knowledge of the genes described herein todesign novel arrays of polynucleotides, cDNAs or genomic DNAs forscreening methods described herein.

In yet other embodiments, the RNA can be detected using microspheres,particles, or bead-based platforms. For example, oligonucleotides thatbind and detect the RNA can be conjugated to beads. In some embodiments,commercially available platforms, such as FlexmiR™ from Luminex (Austin,Tex.), or DASL assay from Illumina (San Diego, Calif.) can be used.

Furthermore, the methods can be performed using a microfluidic device.Such systems miniaturize and compartmentalize processes that allow forbinding and detection of the target RNA. In some embodiments, the RNA isalso isolated from a sample in a microfluidic device. Examples ofmicrofluidic devices that may be used are described in U.S. Pat. Nos.7,591,936, 7,581,429, 7,579,136, 7,575,722, 7,568,399, 7,552,741,7,544,506, 7,541,578, 7,518,726, 7,488,596, 7,485,214, 7,467,928,7,452,713, 7,452,509, 7,449,096, 7,431,887, 7,422,725, 7,422,669,7,419,822, 7,419,639, 7,413,709, 7,411,184, 7,402,229, 7,390,463,7,381,471, 7,357,864, 7,351,592, 7,351,380, 7,338,637, 7,329,391,7,323,140, 7,261,824, 7,258,837, 7,253,003, 7,238,324, 7,238,255,7,233,865, 7,229,538, 7,201,881, 7,195,986, 7,189,581, 7,189,580,7,189,368, 7,141,978, 7,138,062, 7,135,147, 7,125,711, 7,118,910, and7,118,661.

In some embodiments, multiplexing can be performed. For example,multiplexing can be performed using a particle-based assay, such as beadbased assay, in combination with flow cytometry. Multiparametricimmunoassays or other high throughput detection assays using beadcoatings with cognate ligands and reporter molecules with specificactivities consistent with high sensitivity automation can be used. Forexample, in a particle based assay system, a binding agent for an RNA ofinterest, such as an oligonucleotide, can be immobilized on addressablebeads or microspheres. Each binding agent for each individual bindingassay (such as an immunoassay when the binding agent is an antibody) canbe coupled to a distinct type of microsphere (i.e., microbead) and thebinding assay reaction takes place on the surface of the microspheres.Microspheres can be distinguished by different labels, for example, amicrosphere with a specific binding agent would have a differentsignaling label as compared to another microsphere with a differentbinding agent. For example, microspheres can be dyed with discretefluorescence intensities such that the fluorescence intensity of amicrosphere with a specific binding agent is different than that ofanother microsphere with a different binding agent.

The methods of RNA detection can be used to determine the levels of RNAin a sample, such as the mean number of copies per microliter of serum.In some embodiments, the level of each of the RNAs is calculated with a95% confidence interval about the mean (e.g., 15,648 of +/−10,431 copiesper microliter). In other embodiments, the level of each of the RNAs iscalculated with an 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,93, or 94% confidence interval. In yet other embodiments, the level ofeach of the RNAs is calculated with a 95, 96, 97, 98, 99 or 100%confidence interval about the mean.

RNA Patterns and PSA/PCA3 Levels

One or more RNAs can be assessed with one or more non-RNA biomarkers tocharacterize a cancer. A single sample can be used for assessing one ormore RNAs, such as detecting one or more miRNAs, detecting one or moremRNAs, and detecting one or more non-RNA biomarkers. In someembodiments, more than one sample is used. For example, a single sample,such as blood or urine, can be used for detecting one or more miRNAs,PSA mRNA, PCA3 in RNA, and PSA protein.

A combination of an RNA level and a protein level can be used tocharacterize a cancer. In some embodiments, a combination of theexpression level of a mRNA and a mRNA is used. For example, the mRNAlevel can be a of a gene or fusion gene, such as TMPRSS2:ERG orTMPRSS2:ETS. In other embodiments, the mRNA is of PCA or PCA3. In yetother embodiments, the expression levels of one or more miRNA, one ormore mRNA, one or more proteins, or any combination thereof, is used tocharacterize a cancer. In yet other embodiments, the expression levelsof one or more miRNA, one or more mRNA, one or more proteins, or anycombination thereof, is determined for a first sample from a subject,such as urine or blood sample, and used to determine whether a secondsample should be obtained from the subject for further analysis. Forexample, the second sample can be a biopsy.

For example, the expression level of one or more RNAs and of PSA proteincan be used to characterize a prostate cancer. The expression level ofone or more RNAs and of PSA protein can be determined in a first sampleand used to determine whether a second sample, such as a biopsy, shouldbe obtained for further analysis, such as for a histologicalexamination. Assessing an RNA pattern and a PSA protein level canprovide increased specificity or sensitivity in the characterization ofprostate cancer, as compared to assessing the one or more RNAs alone orPSA protein levels alone. For example, the sensitivity, or specificitymay be at least about 5, 10, 15, 20, 30, 35, 40, 50, 75, 100, 150, 200,250, 500, 1000% or more than detection with the one or more RNAs aloneor PSA protein level alone.

In some embodiments, a PCA3 level is used to characterize prostatecancer or determine whether a second sample, such as a biopsy, should beobtained for analysis. For example, in some embodiments, a miRNA leveland a PCA3 mRNA level are used. Assessing a miRNA level and PCA3 mRNAlevel can provide increased specificity or sensitivity in thecharacterization of prostate cancer, as compared to assessing the miRNAlevel alone or the PCA3 mRNA level alone. For example, the sensitivityor specificity may be at least about 5, 10, 15, 20, 30, 35, 40, 50, 75,100, 150, 200, 250, 500, 1000% or more.

In yet other embodiments, a miRNA level, PCA3 mRNA level, and PSA mRNAlevel are used to characterize prostate cancer or determine whether asecond sample, such as a biopsy, should be obtained for analysis.Assessing a miRNA level, PCA3 mRNA level, and PSA mRNA levels canprovide increased specificity or sensitivity in the characterization ofprostate cancer, as compared to assessing 1 or 2 of the following: miRNAlevel, PCA3 mRNA level, and PSA mRNA level. For example, the sensitivityor specificity may be at least about 5, 10, 15, 20, 30, 35, 40, 50, 75,100, 150, 200, 250, 500, 1000% or more.

In yet other embodiments, a miRNA level, PCA3 mRNA level, PSA mRNAlevel, and PSA protein level are used to characterize prostate cancer ordetermine whether a second sample, such as a biopsy, should be obtainedfor analysis. Assessing a miRNA level; PCA3 mRNA level, and PSA mRNAlevel can provide increased specificity or sensitivity in thecharacterization of a prostate cancer, as compared to assessing 1, 2, or3 of the following: miRNA level, PCA3 mRNA level, PSA mRNA level, andPSA protein level. For example, the sensitivity or specificity may be atleast about 5, 10, 15, 20, 30, 35, 40, 50, 75, 100, 150, 200, 250, 500,1000% or more.

In some embodiments, the PCA3 mRNA level and PSA mRNA level are used tocreate a PCA3 score, which is a ratio of PCA3 mRNA level to PSA mRNAlevel, such as PCA3 mRNA copy number compared to PSA mRNA copy numbers.The PCA3 score can be used to characterize a prostate cancer ordetermine whether a second sample, such as a biopsy, should be obtainedfor analysis.

In some embodiments, the PCA3 score is used with the expression level ofone or more RNAs, such as the level of a miRNA, to characterize aprostate cancer or determine whether a second sample, such as a biopsy,should be obtained for analysis. Assessing an RNA pattern and PCA3 scorecan provide increased specificity or sensitivity in the characterizationof prostate cancer, as compared to assessing the one or more RNAs aloneor PCA3 score alone. For example, the sensitivity, or specificity may beat least about 5, 10, 15, 20, 30, 35, 40, 50, 75, 100, 150, 200, 250,500, 1000% or more.

In yet other embodiments, the PCA3 score is used with the expressionlevel of one or more RNA and PSA protein to characterize a prostatecancer or determine whether a second sample, such as a biopsy, should beobtained for analysis. Assessing one or more RNAs and PSA protein anddetermining a PCA3 score can provide increased specificity orsensitivity in the characterization of prostate cancer, as compared toassessing 1 or 2 of the following: an RNA pattern, PSA protein level,and PCA3 score. For example, the sensitivity, or specificity may be atleast about 5, 10, 15, 20, 30, 35, 40, 50, 75, 100, 150, 200, 250, 500,1000% or more.

In yet other embodiments, prostate cancer is characterized bydetermining a product value by multiplying the level of an RNA with thelevel of PSA. The product value can then be used to characterize aprostate cancer. The product value can be used to diagnose a subject, toclassify a cancer as benign or malignant, or to select a therapy for thesubject. The product value for a subject can be compared to a referencevalue to characterize the cancer. For example, a reference value can bedetermined for diagnosing prostate cancer by determining the productvalue for patients with prostate cancer. Reference values can also bedetermined for different stages or prostate cancer, or for benignprostate cancer or malignant prostate cancer. Reference values can alsobe determined for drug efficacy, such as by determining reference valuesbased on patients on effective prostate cancer therapeutics.

The product value can be used to characterize a prostate cancer with atleast about 70% or 75% specificity. For example, a prostate cancer canbe characterized using a product value with greater than about 76, 77,78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,96, or 97% specificity. The prostate cancer can be characterized with atleast about 97.1, 97.2, 97.3, 97.4, 97.5, 97.6, 97.7, 97.8, 97.8, 97.9,98.0, 98.1, 98.2, 98.3, 98.4, 98.5, 98.6, 98.7, 98.8, 98.9, 99.0, 99.1,998.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8, 99.9% specificity. In yetother embodiments, the cancer can be characterized with 100%specificity.

In some embodiments, the cancer can be characterized using a productvalue with at least about 60% sensitivity, such as at least about 60,65, 70, 75, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94,95, 96, or 97% sensitivity. The cancer can be characterized with atleast about 97.1, 97.2, 97.3, 97.4, 97.5, 97.6, 97.7, 97.8, 97.8, 97.9,98.0, 98.1, 98.2, 98.3, 98.4, 98.5, 98.6, 98.7, 98.8, 98.9, 99.0, 99.1,99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8, 99.9% sensitivity. In yetother embodiments, the cancer can be characterized with 100%sensitivity. Furthermore, the product value can be used to characterizea prostate cancer with 100% specificity and 100% sensitivity. Forexample, a diagnosis of prostate cancer can be provided with 100%specificity and 100% sensitivity.

The level of RNA can be the number of copies of the miRNA per microliterof a sample and the level of PSA can be the amount of protein permicroliter of sample, such as ng/ml. The amount of miRNA multiplied bythe amount of PSA protein in a sample can be used to determine a productvalue for normal subjects and for subjects with prostate cancer. Thus,reference levels can be determined for normal subjects and for subjectswith prostate cancer. The product value for a sample obtained from asubject can be determined and compared to the reference levels tocharacterize a cancer for the subject, such as provide a diagnosis. Forexample, a product value can be determined by multiplying the copies permicroliter of miR-141 in a serum sample by the nanogram per microlitersof PSA in a serum sample (see for example, FIG. 5). If the product valueis less than 1500, 1550, 1400, 1450, or 1400, a diagnosis that thesubject does not have prostate cancer can be provided. Alternatively, ifthe product value is greater than 1500, 1600, 1700, 1800, 1900 or 2000,a diagnosis that the subject has prostate cancer can be provided. Insome embodiments, if the product value is greater than about 2000, 2100,2200, or 2300, a diagnosis that the subject has prostate cancer isprovided. A prostate cancer can be classified as benign if the productvalue is less than 1500. Alternatively, if the product value is greaterthan 1500, the cancer can be classified as malignant.

The product value can be used to classify the prostate cancer ordetermine whether a second sample, such as a biopsy should be obtained,for analysis. For example, if the product value is less than 1500, 1200,or 1000, a biopsy would not be obtained. In other embodiments, if theproduct value was greater than 1500, 1700, 1800, or 2000, a biopsy wouldbe obtained.

In another embodiment, a method to classify a prostate cancer as benignor malignant as well as to determine whether a second sample should beobtained. For example, when the PSA protein is less than about 3 ng/mL,such as at least 2.9, 2.8, 2.7, 2.6, 2.5, 2.4, 2.3, 2.2, 2.1, or 2.0ng/mL, the miRNA is less than about 3000 copies per microliter, such asless than about 2500, 2000, 1500, 1000 or 500, and optionally, the PCA3score is less than 35, such as less than 30, 25, or 20, the prostatecancer is classified as benign, a second sample, such as biopsy, is notobtained, or both.

In another embodiment, when the miRNA is less than about 3000 copies permicroliter, such as less than about 2500, 2000, 1500, 1000 or 500, andthe PCA3 score is less than 35, such as less than 30, 25, or 20, theprostate cancer is classified as benign, a second sample, such asbiopsy, is not obtained, or both.

When the PSA protein is greater than about 4 ng/mL, such as at least4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9 or 5.0 ng/mL, the miRNA isgreater than about 9000 copies per microliter, such as greater thanabout 9500, 10,000, 15,000 or 20,000, and optionally, the PCA3 score isgreater than 35, such as at least 40, 45, or 50, the prostate cancer isclassified as malignant, a second sample, such as biopsy, is obtained,or both.

In another embodiment, when the miRNA is greater than about 9000 copiesper microliter, such as greater than about 9500, 10,000, 15,000 or20,000, and the PCA3 score is greater than 35, such as at least 40, 45,or 50, the prostate cancer is classified as malignant, a second sample,such as biopsy, is obtained, or both.

Detection System and Kits

Also provided is a detection system configured to determine one or moreRNAs for characterizing a cancer. For example, the detection system canbe configured to assess at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25,30, 40, 50, 60, 70, 80, 90, 100, 1000, 2500, 5000, 7500, 10,000,100,000, 150,000, 200,000, 250,000, 300,000, 350,000, 400,000, 450,000,500,000, 750,000, or 1,000,000 RNAs. For example, the detection systemcan be configured to assess 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30,40, 50, 60, 70, 80, 90, 100, 1000, 2500, 5000, 7500, 10,000, 100,000,150,000, 200,000, 250,000, 300,000, 350,000, 400,000, 450,000, 500,000,750,000, 1,000,000 or more miRNAs, wherein one or more of the miRNAs areselected from Table 1. In some embodiments, the one or more miRNAsdetected by the system are selected from the group consisting of:miR-629, miR-671-3p, miR-9, miR-491, miR-182, miR125a-3p, miR-324-5p,miR-148b, miR-222, miR-141. In yet other embodiments, the one or moremiRNAs are selected from the group consisting of miR-99, miR-101,miR-130, miR-135, miR-141, miR-148, miR-182, miR-186, miR-206, miR-320,miR-374, miR-433, miR-496, miR-517, miR-590, miR-620, miR-768, miR-223,miR-203, miR-199, miR-519, miR-302, miR-30, miR-200, miR-23, miR-29,miR-181, miR-548 or miR-370. The detection system can also be configuredto detect the mRNA levels of PSA, PCA or both.

The detection system can be a low density detection system or a highdensity detection system. For example, a low density detection systemcan detect up to about 100, 200, 300, 400, 500, or 1000 RNA, whereas ahigh density detection system can detect at least about 2000, 3000,4000, 5000, 6000, 7000, 8000, 9,000, 10,000, 15,000, 20,000; 25,000,50,000, or 100,000 RNAs. The detection system can be specific fordetecting a species of RNA, such as miRNAs. A low density detectionsystem for miRNA can detect up to about 100, 200, 300, 400, 500, or 1000miRNAs. A high density detection system for miRNA can detect at leastabout 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9,000, 10,000, 15,000,20,000, 25,000, 50,000, or 100,000 miRNAs.

The detection system can comprise a set of probes that selectivelyhybridizes to the one or more of the RNAs. For example, the detectionsystem can comprise a set of probes that selectively hybridizes to atleast 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50, 60, 70, 80,90, 100, 1000, 2500, 5000, 7500, 10,000, 100,000, 150,000, 200,000,250,000, 300,000, 350,000, 400,000, 450,000, 500,000, 750,000, or1,000,000 miRNAs. For example, the set of probes can selectivelyhybridize to or more miRNAs selected from Table 1, one or more miRNAsare selected from the group consisting of: miR-629, miR-671-3p, miR-9,miR-491, miR-182, miR125a—3p, miR-324-5p, miR-148b, miR-222, miR-141. Inyet other embodiments, the one or more miRNAs are selected from thegroup consisting of miR-99, miR-101, miR-130, miR-135, miR-141, miR-148,miR-182, miR-186, miR-206, miR-320, miR-374, miR-433, miR-496, miR-517,miR-590, miR-620, miR-768, miR-223, miR-203, miR-199, miR-519, miR-302,miR-30, miR-20, miR-200, miR-23, miR-29, miR-18 miR-548 or miR-370. Thedetection system can also comprise probes for detecting the mRNA levelsof PSA, PCA or both.

The detection system can be a low density detection system or a highdensity detection system comprising probes to detect the RNAs. Forexample, a low density detection system can comprise probes to detect upto about 100, 200, 300, 400, 500, or 1000 RNA, whereas a high densitydetection system can comprise probes to detect at least about 2000,3000, 4000, 5000, 6000, 7000, 8000, 9,000, 10,000, 15,000, 20,000,25,000, 50,000, or 100,000 RNAs. The probes can be specific fordetecting a species of RNA, such as miRNAs, such that a low densitydetection system for miRNA can comprise probes for detecting up to about100, 200, 300, 400, 500, or 1000 miRNAs. A high density detection systemfor miRNA can comprise probes for detecting at least about 2000, 3000,4000, 5000, 6000, 7000, 8000, 9,000, 10,000, 15,000, 20,000, 25,000,50,000, or 100,000 miRNAs.

The probes may be attached to a solid substrate, such as an array orbead. Alternatively, the probes are not attached. The detection systemmay be an array based system, a sequencing system, a PCR-based system,or a bead-based system, such as described above. The detection systemmay be part of a kit. Alternatively, the kit may comprise the one ormore probe sets described herein. For example, the kit may compriseprobes for detecting one or more of the miRNAs selected from the groupconsisting of: miR-629, miR-671-3p, miR-9, miR-491, miR-182, miR125a-3p,miR-324-5p, miR-148b, miR-222, or miR-141. In yet other embodiments, theone or more miRNAs are selected from the group consisting of: miR-99,miR101, miR-130, miR-135, miR-141, miR-148, miR-182, miR-186, miR-206,miR-320, miR-374, miR-433, miR-496, miR-517, miR-590, miR-620, miR-768,miR-223, miR-203, miR-199, miR-519, miR-302, miR-30, miR-20, miR-200,miR-23, miR-29, miR-181, miR-548 or miR-370. In some embodiments, thekit further comprises one or more reagents that selectively hinds to PSAor PCA3. For example, the kit may comprise a reagent, such as a probe,to detect PSA protein levels or PSA mRNA levels. The kit may alsocomprise a reagent to detect PCA3 mRNA levels.

Computer System

Also provided herein, is a computer system for characterizing a cancer.Accordingly, FIG. 6 is a block diagram showing a representative examplelogic device through which a phenotype profile and report may begenerated.

FIG. 6 shows a computer system (or digital device) 600 to receive theexpression level data from a biological sample, analyze the expressionlevels, determine a characteristic for a cancer (such as, but notlimited to, classifying a cancer, determining whether a second sampleshould be obtained, providing a diagnosis, providing a prognosis,selecting a treatment, determining a drug efficacy), and produce theresults, such as an output on the screen, printed out as a report, ortransmitted to another computer system. The computer system 600 may beunderstood as a logical apparatus that can read instructions from media611 and/or network port 605, which can optionally be connected to server609 having fixed media 612. The system shown in FIG. 6 includes CPU 501,disk drives 603, optional input devices such as keyboard 615 and/ormouse 616 and optional monitor 607.

Data communication can be achieved through the indicated communicationmedium to a server 609 at a local or a remote location. Thecommunication medium can include any means of transmitting and/orreceiving data. For example, the communication medium can be a networkconnection, a wireless connection or an internet connection. Such aconnection can provide for communication over the World Wide Web. It isenvisioned that data relating to the present invention, such as theexpression levels of the one or more RNAs, the results of the analysisof the expression levels (such as the characterizing or classifying ofthe cancer), can be transmitted over such networks or connections forreception and/or review by a party 622. The receiving party 622 can be,but is not limited, to a subject, a health care provider or a healthcare manager. In some embodiments, the information is stored on acomputer-readable medium.

EXAMPLES Example 1 Obtaining Serum Samples from Subjects

Blood is collected from subjects (both healthy subjects and subjectswith prostate cancer) in EDTA tubes, citrate tubes or in a 10-mlVacutainer SST plus Blood Collection Tube (BD367985 or BD366643, BDBiosciences). Blood is processed for plasma isolation within 2 h ofcollection.

Samples are allowed to sit at room temperature for a minimum of 30 minand a max of 2 h. Separation of the clot is accomplished bycentrifugation at 1,000-1,300×g at 4° C. for 15-20 min. The serum isremoved and dispensed in aliquots of 500 μl into 500- to 750-μlcryo-tubes. Specimens are stored at −80° C.

At a given sitting, the amount of blood drawn can range from ˜20 to ˜90ml. Blood from several EDTA tubes is pooled and transferred toRNase/DNase-free 50-ml conical tubes (Greiner), and centrifuged at1,200×g at room temperature in a Hettich Rotanta 460R benchtopcentrifuge for 10 min. Plasma is transferred to a fresh tube, leavingbehind a fixed height of 0.5 cm plasma supernatant above the pellet toavoid disturbing the pellet. Plasma is aliquoted, with inversion to mixbetween each aliquot, and stored at −80° C.

Example 2 RNA Isolation from Human Plasma and Serum Samples

Four hundred μl of human plasma or serum is thawed on ice and lysed withan equal volume of 2× Denaturing Solution (Ambion). RNA is isolatedusing the mirVana PARIS kit following the manufacturer's protocol forliquid samples (Ambion), modified such that samples are extracted twicewith an equal volume of acid-phenol chloroform (as supplied by theAmbion kit). RNA is eluted with 105 μl of Ambion elution solutionaccording to the manufacturer's protocol. The average volume of eluaterecovered from each column is about 80 μl.

A scaled-up version of the mirVana PARIS (Ambion) protocol is also used:10 ml of plasma is thawed on ice, two 5-ml aliquots are transferred to50-ml tubes, diluted with an equal volume of mirVana PARIS 2× DenaturingSolution, mixed thoroughly by vortexing for 30 s and incubated on icefor 5 min. An equal volume (10 ml) of acid/phenol/chloroform (Ambion) isthen added to each aliquot. The resulting solutions are vortexed for 1min and spun for 5 min at 8,000 rpm, 20° C. in a JA17 rotor. Theacid/phenol/chloroform extraction is repeated three times. The resultingaqueous volume is mixed thoroughly with 1.25 volumes of 100%molecular-grade ethanol and passed through a mirVana PARIS column insequential 700-μl aliquots. The column is washed following themanufacturer's protocol, and RNA is Owed in 105 μl of elution buffer(95° C.). A total of 1.5 μl of the eluate is quantified by Nanodrop.

Example 3 Measurement of miRNA Levels in RNA from Plasma and Serum byUsing TaqMan qRT-PCR Assays

A fixed volume of 1.67 μl of RNA solution from about ˜80 μl-eluate fromRNA isolation of a given sample is used as input into the reversetranscription (RT) reaction. For samples in which RNA is isolated from a400-μl plasma or serum sample, for example, 1.67 μl of RNA solutionrepresents the RNA corresponding to (1.67/80)×400=8.3 μl plasma orserum. For generation of standard curves of chemically synthesized RNAoligonucleotides corresponding to known miRNAs, varying dilutions ofeach oligonucleotide are made in water such that the final input intothe RT reaction has a volume of 1.67 μl. Input RNA is reversetranscribed using the TaqMan miRNA Reverse Transcription Kit andmiRNA-specific stem-loop primers (Applied BioSystems) in a small-scaleRT reaction comprised of 1.387 μl of H2O, 0.5 μl of 10×Reverse-Transcription Buffer, 0.063 of RNase-Inhibitor (20 units/μl),0.05 μl of 100 mM dNTPs with dTTP, 0.33 μl of MultiscribeReverse-Transcriptase, and 1.67 μl of input RNA; components other thanthe input RNA can be prepared as a larger volume master mix, using aTetrad2 Peltier Thermal Cycler (BioRad) at 16° C. for 30 min, 42° C. for30 min and 85° C. for 5 min. Real-time PCR is carried out on an AppliedBioSystems 7900HT thermocycler at 95° C. for 10 min, followed by 40cycles of 95° C. for 15 s and 60° C. for 1 min. Data is analyzed withSDS Relative Quantification Software version 2.2.2 (AppliedBioSystems.), with the automatic Ct setting for assigning baseline andthreshold for Ct determination.

The protocol can also be modified to include a preamplification step,such as for detecting miRNA. A 1.25-μl aliquot of undiluted RT productis combined with 3.75 μl of Preamplification PCR reagents [comprised,per reaction, of 2.5 μl of TaqMan PreAmp Master Mix (2×) and 1.25 μl of0.2×TaqMan miRNA Assay (diluted in TE)] to generate a preamplificationPCR, which is carried out on a Tetrad2 Peltier Thermal Cycler (BioRad)by heating to 95° C. for 10 min, followed by 14 cycles of 95° C. for 15s and 60° C. for 4 min. The preamplification PCR product is diluted (byadding 20 ml of H2O to the 5-μl preamplification reaction product),following which 2.25 μl of the diluted material is introduced into thereal-time PCR and carried forward as described.

Example 4 Generation of Standard Curves for Absolute Quantification ofmiRNAs

Synthetic single-stranded RNA oligonucleotides corresponding to themature miRNA sequence (miRBase Release v.10.1) are purchased from Sigma.Synthetic miRNAs are input into the RT reaction over anempirically-derived range of copies to generate standard curves for eachof the miRNA TaqMan assays listed above. In general, the lower limit ofaccurate quantification for each assay is designated based on theminimal number of copies input into an RT reaction that results in a Ctvalue within the linear range of the standard curve and that is also notequivalent to or higher than a Ct obtained from an RT input of lowercopy number. A line is fit to data from each dilution series using Ctvalues within the linear range, from which y=mln(x)+b equations arederived for quantification of absolute miRNA copies (x) from each sampleCt (y). Absolute copies of miRNA input into the RT reaction areconverted to copies of miRNA per microliter plasma (or serum) based onthe knowledge that the material input into the RT reaction correspondsto RNA from 2.1% of the total starting volume of plasma [i.e., 1.67 μlof the total RNA eluate volume (80 μl on average) is input into the RTreaction]. An example of a synthetic miRNA sequence is for miR-141,5′UAACACUGUCUGGUAAAGAUGG3′ (SEQ ID NO. 1), which can be obtainedcommercially such as from Sigma (St. Louis, Mo.).

Example 5 Identification of Gene Expression Profiles for Prostate CancerUsing Immunohistochemistry Analysis

Samples of solid tumor are excised and subjected to fixation andembedded in paraffin. The tumor block is cut into sections for placementon a glass slide. The slide is stained with the designated primaryantibody which reacts with the tissue antigen as chosen by thepathologist. A labeled secondary antibody is reacted with the primaryantibody and coupled to a streptavidin-horseradish peroxidase. Thiscomplex is reacted with a chromogen to produce a colored stain. Thestained slides are viewed by a pathologist under a light microscope. Thepathologist performs a semi-quantitative interpretation of the intensityof the staining. Typically, a 0 to 4 scale is utilized with 0representing no staining or negative result. The pathologist thenestimates the proportion of the tumor cells that are stained positively.Typically, a 0 to 100% scale is utilized. Each antibody interpretationis annotated by the pathologist into the patient report. Results of theanalysis of the 22 prostate cancer samples shows the genes overexpressedin at least 10 of the 22 samples are androgen receptor, EGFR, HSP90, andSPARC (FIG. 1C).

Example 6 Tissue Preparation for Identification of Gene ExpressionProfiles for Prostate Cancer

Tissue Preparation

Before starting, and using powder-free gloves, the work area isthoroughly cleaned with either RNaseAway® (Sigma Cat. No. 83931) or 70%ethanol (70% 200proof ethanol and 30% pure water). Frozen tissue fromthe −80° C. freezer is removed and is immediately transferred to a traycontaining dry ice, the tissue does not remain at room temperature forany length of time. Particularly if the tissue is small, as thawingcould occur quickly and consequently the RNA would degrade irreversibly.

A sterile 100 mm diameter Petri dish (plastic) or tissue culture dish isplaced on the clean ice to pre-chill, as well as the clean serrated tipforceps, and a new, clean heavy duty razor blade.)

The tissue in the dish; if wrapped in foil or other material, iscarefully unwrapped while in contact with the ice to prevent it fromthawing. Even partial thawing of the tissue (which could happen isseconds) will irreversibly degrade the RNA, compromising the quality ofthe microarray assay or making it difficult to assay.

While using pre-chilled forceps and a razor blade, small pieces are cutoff of the tissue so the sections to be used for microarray are notlarger than approximately 1 mm thick. Often “shaving” off parts of thetumor is the easiest and fastest method. The forceps and razor blade arechilled every few seconds on a piece of dry ice so they remain very coldwhen in contact with the tissue. About 100-400 mg of tissue, roughly 20mm³, no larger than “pea-size” is used.

The tissue cuttings are carefully placed into an anti-static weight dish(preferably the “pour boat type”) previously chilled on the dry ice.Then, the tissue is quickly transferred from the weigh dish to apre-chilled borosilicate tube that has been previously marked with theappropriate specimen number, ensuring the cut tissue pieces do not stickto the walls of the tube, since they would rapidly thaw. Keeping thetube very cold and upright when transferring tissue to it is the bestway to avoid that.

Any leftover tissue should be kept frozen on the dry ice until returnedto a −80° C. freezer.

Homogenization Using the Covaris Tissue Processor

First, the circulating water bath (Multitemp III) is turned on, so itstarts cooling off the water. Make sure the water bath contains enoughwater (ultrapure water only). The Covaris S-2 instrument is turned on.The water chamber of Covaris system is filled with 95% ultrapure waterand 5% tap water. The computer connected to Covaris S-2 instrument isturned on, and the SonoLab software is opened.

The degassing process is turned on by clicking on the “degas” buttonwithin the SonoLab window; water should be degassed and pre-chilled (bythe Multitemp III chiller water bath) for about 30 minutes, sotemperature will remain between 17 and 20° C. during the homogenizationof the samples. Also, the degassing process should be running during theentire session, and turned off only when ready to shut down the SonoLabsoftware and the Covaris S-2 instrument.

The previously cut frozen tissue remains in the Covaris borosilicatetube, on the dry ice, until everything is ready for homogenization.

The program “MPI/IGC Processing” in the SonoLab program is opened.(NOTE: The following steps are done very quickly so the frozen tissueremains frozen until the last second before homogenization. The longerthe tissue is thawed in between steps, the more RNA degradationtypically occurs.)

Using a filtered 1000 μL pipet tip and a P-1000 pipetor, 500 μL of RLTbuffer (from the Qiagen RNeasy mini kit) is added to the frozen tissue.Immediately, the screw cap is put back on and very quickly the tube isinserted into the tube holder in the Covaris S-2 instrument.2-Mercaptoethanol is added to RLT before use. Ten ML of2-Mercaptoethanol is added per 1 mL RLT buffer. Then the Start button tocommence the homogenization is pressed.

The tube is removed after the process is completed, and is placed on wetice. The cap is opened and 500 μL of TRIzol is added. The tube is thenrecapped and is quickly mixed by moving the tube side to side.

If RNA extraction is performed shortly after homogenization, the tubesremain on wet ice, otherwise all specimens are frozen in dry ice or at−80° C. until ready for RNA extraction.

When the homogenization session ends, the degassing is shut off, thewater is removed from the water chamber in the Covaris S-2 instrument,then degas for about 2 seconds in order to purge the remaining waterfrom the lines. The SonoLab program is closed first, and then theMultitemp III chiller water bath, and Covaris S-2 instrument are shutoff.

Example 7 RNA Extraction and Purification for Identification of GeneExpression Profiles for Prostate Cancer

TRIzol Extraction.

If the previously homogenized tissue has been stored in the −80° C.freezer, the tissue is thawed at room temperature or 65° C. Using cleanpowder-free gloves, the work area is cleaned again thoroughly witheither RNaseAway® (Sigma Cat. No. 83931) or 70% ethanol. (NOTE: thefollowing steps will be performed at room temperature and with roomtemperature reagents, unless otherwise indicated)

Tube contents are transferred to a 2 mL screw-cap, sterile andRNAse-free tube, ensuring that the lids are well tightened. The sampleis heated up in a digital heat block at 65° C. for 5 minutes. Ifpreviously frozen, the sample is incubated at 65° C. for 7 minutes.

The sample is then removed from heat, and immediately, 200 μL ofchloroform is added while the tubes are still hot. The caps aretightened well and are then mixed by shaking vigorously for 15-30 sec(do not vortex or DNA molecules will be sheared and may contaminate theRNA).

The tubes are then cooled on ice for 5 minutes, then the tubes arecentrifuged at 10,000×g for 10 minutes at room temperature. Slowly, andusing a filtered tip, approximately 0.7 mL of the upper aqueous phasewhich contains the total RNA is removed and is placed in a new, labeled1.5 mL tube.

0.7 mL of room-temperature 70% ethanol is then added to the homogenizedlysate, and is mixed well by pipetting.

Purification of the RNA-containing aqueous phase with RNeasy mini ormicro kit. (NOTE: When processing needle biopsy samples, micro columnsare used to bind the RNA and carrier RNA added to the lysate. The RNeasyMicro kit (Qiagen Cat. No. 74004) contains poly-AN RNA to be added ascarrier RNA. Before using for the first time, dissolve the carrier RNA(310 μg) in 1 mL RNase free water. Store this stock solution at −20° C.,and use to make fresh dilutions for each set of RNA preps.)

To make a working solution (4 ng/μL) for 10 preps, 5 μL of the dissolvedRNA is added to 34 μL of Buffer RLT and is mixed by pipetting. 6 μL ofthis diluted solution is added to 54 μL of Butler RLT. The finalconcentration is 4 ng/μL.

Up to 0.7 mL of the sample, including any precipitate that may haveformed, is applied to an RNeasy mini or micro column placed in a 2 mLcollection tube. The tube is closed gently, and is centrifuged for 30seconds at 8000×g. The remaining 0.7 mL of the sample mixture is addedto the same RNeasy mini or micro column and again is centrifuged at8000×g for 30 seconds.

0.7 mL of buffer RW1 is then added to the RNeasy mini or micro column.The tube is closed gently, and is centrifuged for 30 seconds at 8000×gto wash the column. The flow through and 2 mL collection tube isdiscarded.

Without touching the bottom part of the column, the RNeasy mini or microcolumn is transferred into a new 2 mL collection tube. 0.5 mL buffer RPEis pipetted onto the RNeasy mini or micro column. The tube is closedgently, and is centrifuged for 30 seconds at 8000×g to wash the column.The flow through is then discarded.

Again, 0.5 mL buffer RPE is added to the RNeasy column. The tube isclosed gently, and is centrifuged for 2 minutes at 8000×g to dry theRNeasy silica-gel membrane. The flow through and the collection tube arethen discarded.

To elute, the RNeasy mini or micro column are transferred to a new 1.5mL collection tube (this tube is labeled with the case number). RNasefree H2O (30-40 μL for a mini column or 7-14 μL for a micro column) ispipetted above the center of the RNeasy silica-gel membrane, withouttouching it. The tube is closed and after 2-4 minutes, the tube iscentrifuged at 16,100×g for 1 minute.

The mini or micro column is then discarded and the RNA is placed on ice.

1 μL of each sample is aliquoted into a PCR tube for bio-analyzing. TheRNA concentration determined by measuring the optical density orabsorbance in a spectrophotometer as follows: TE pH 8.0 is used as thediluent buffer and as the blank. A 1:100 dilution: 1 μL RNA with 99 μLTE pH 8.0 is made and the absorbance for 260 and 280 nm is read with anAgilent spectrophotometer using a quartz cuvette. The setting in thespectrophotometer is at “Ratio,” and the ration obtained is theabsorbance at 260 over 280, which ideally ranges from 1.8 to 2.2. Incase absorbance at 260 nm is out of the linear range (below 0.1 or above1), the dilution of the RNA in TE is repeated either by increasing thequantity of RNA or diluting it further, respectively. The RNA is thenplace in a designated freezer at −80° C. until ready to proceed with RNAlabeling.

Example 8 RNA Amplification and Fluorescent Labeling for Identificationof Gene Expression Profiles for Prostate Cancer

Following RNA purification from a tissue, the amplification and labelingor this RNA is a key step in gene expression profiling using microarrayanalysis. This technique allows the use of purified total RNA as atemplate for the synthesis of complementary DNA (cDNA) by reversetranscription the first step in RNA amplification. Fluorescentcomplementary RNA (cRNA) is synthesized by in vitro transcription, usingcDNA as a template while incorporating a nucleotide (CTP) coupled to afluorescent cyanine dye (cyanine-3 (pink) or cyanine-5 (blue)). Theresulting fluorescent RNA is then compared side by side with anotherRNA, labeled with a different cyanine dye, by hybridizing both to a cDNAarray.

A) cDNA Synthesis from Total RNA:

Before starting, and using powder-free gloves, the work area is cleanedthoroughly with either RNaseAway® (Sigma Cat. No. 83931) or 70% ethanol(70% 200proof ethanol and 30% pure water). It is very important that thework area, the materials and equipment used are very clean, dust- andRNAse-free.

2 μg total RNA is added to a volume of 10.3 μL to a 0.2 mLmicrocentrifuge tube. The total concentration should be at least 5ng/μL. When using more than 500 ng total RNA (or 10 ng or more or polyA+RNA) the total volume should be 6.5 μL.

3 μL of T7 Promoter Primer (from kit) is then added. Nuclease-free wateris then used to bring the total reaction volume to 11.5 μL. The primerand the template are denatured by incubating the reaction at 65° C. in athermal cycler for 10 minutes. The reactions are incubated at 4° C. for5 minutes (this can be done on ice or in the thermal cycler).

Immediately-prior to use, the following components shown in Table 2 aregently mixed by pipetting, in the order indicated, at room temperature(pre-warm the 5× First Strand Buffer by incubating the vial in an 80° C.heat block for 1-2 minutes). To ensure optimal re-suspension, vortexbriefly and spin the tube briefly in a microcentrifuge at full speed todrive the contents off the walls and lid. Keep at room temperature untiluse.

TABLE 2 cDNA Master Mix Component Vol. (μL/rxn) Vol. (μL/6.5 rxn) 5XFirst Strand Buffer 4.0 26 0.1 M DTT 2.0 13 10 mM dNTP mix 1.0 6.5 MMLVRT 1.0 6.5 RNaseOUT 0.5 3.3 TOTAL VOLUME 8.5 55.3

To each sample tube, 8.5 μL of the cDNA Master Mix is added. The tubesare then vortexed at a low setting with short pulses in order to avoidbubble formation. The presence of bubbles could lead to enzymedenaturation thereby impairing enzyme activity.

The samples are then incubated at 40° C. in a thermal cycler for 2hours. The temperature of the thermocycler is then switched to 65° C.and the samples are incubated for 15 minutes (incubation at 65° C.inactivates MMLV-RT (Moloney murine leukemia virus reversetranscriptase)).

The reactions are then incubated at 4° C. for 5 minutes (this can bedone on ice or in the thermal cycler). The samples are spun briefly in amicrocentrifuge at full speed to drive tube contents off the tube walland lid.

B. Fluorescent cRNA Synthesis: In Vitro Transcription and Incorporationof Cyanine 3- or Cyanine 5-CTP

To each sample tube, either 2.4 μL cyanine 3-CTP (10 mM) or 2.4 μLcyanine 5-CTP (10 mM) is added. Cyanine 3 is bright pink and cyanine 5is bright blue. Both are light sensitive and thus light exposure shouldbe minimized. The cyanine 3-CTP (pink) is typically used for normalreference RNA labeling, and cyanine 5-CTP (blue) for the patient (tumor)RNA labeling. The 50% PEG (polyethylene glycol) solution is pre-warmedby incubating the vial in a 40° C. heat block for one minute. To ensureoptimal re-suspension, vortex briefly and spin the tube briefly in amicrocentrifuge at full speed to drive the contents off the tube wallsand lid. The tube is kept at room temperature until use.

A Transcription Master Mix is made as shown in Table 3.Immediately-prior to use, quickly spin all tubes containing reactioncomponents to bring down contents (for a few seconds), and combine thefollowing components in the order indicated, at room temperature (thengently vortex Master Mix on a low setting, and spin in a microcentrifugeat full speed before adding to sample tubes). (Note: The enzymes are notadded until just before performing the reaction).

TABLE 3 Transcription Master Mix Component Vol. (μL/rxn) Vol. (μL/6.5rxn) Nuclease-free water 15.3 99.4 4X Transcription Buffer 20 130 0.1 MDTT 6.0 39 NTP Mix 8.0 52 50% PEG 6.4 41.6 RNA seOUT 0.5 3.3 InorganicPyrophosphatase 0.6 3.9 T7 RNA Polymerase 0.8 5.2 TOTAL VOLUME 57.6374.4

To each sample tube, 57.6 μL of Transcription Master Mix is added andmixed by carefully vortexing at a low setting with short pulses in orderto avoid bubble formation. The tubes are then quickly spun in amicrocentrifuge at full speed to bring down contents of tube (for a fewseconds).

The samples are then incubated in a thermal cycler bath at 40° C. for 2hours.

C. Purification of Amplified cRNA (Note: Remember to add four volumes of100% ethanol to Buffer RPE before using the kit for the first time (Seebottle label for specific volume)).

20 μL of nuclease free-water is added to the cRNA sample to obtain atotal volume of 100 μL. 350 μL of Buffer RLT is added and is then mixedthoroughly by gently vortexing. 250 μL of ethanol (100% purity) is addedand is then mixed thoroughly by vortexing. The sample is not centrifugedafter.

700 μL of the cRNA sample is added to an RNeasy mini column in a 2 mLcollection tube. The sample is centrifuged for 30 seconds at 13,000×g.After this first centrifugation, color should be present in the columnmembrane if the labeling is successful (pink for cyanine-3 and blue forcyanine-5).

The sample is passed through the column a second time. This allows thecapture of labeled RNA not retained by the membrane in the first pass.The flow-through and collection tube is then discarded.

The RNeasy column is then transferred to a new collection tube and 500μL of buffer RPE is added to the column. The sample is then centrifugedfor 30 seconds at 13,000×g. The flow through is then discarded and thecollection tube is re-used.

Again, 500 μL of Buffer RPE is added to the column. The sample is thencentrifuged for 1 minute at 13,000×g, and the flow through and thecollection tube is discarded.

The cleaned cRNA sample is eluted by transferring the RNeasy column to anew 1.5 mL collection tube. 30 μL of RNase-free water is added directlyonto the RNeasy filter membrane. After 2-3 minutes the tube iscentrifuged for 30 seconds at 13,000 rpm. The flow-through and thecollection tube is retained (this is the labeled cRNA; a pink (cyanine3) or blue (cyanine 5) color should be present).

The RNA concentration is determined by measuring the optical density orabsorbance in a spectrophotometer (Agilent Technologies) as follows: TEpH 8.0 is used as the diluent buffer and as the blank. A 1:20 dilution:4 μl RNA with 76 μl TE pH 8.0 is prepared. Absorbance for 260 (RNA), 550(cyanine 3), and 650 (cyanine 5) nm in the Agilent spectrophotometer isdetermined using a quartz cuvette. The setting in the spectrophotometeris at “Spectrum/Peaks” and the range is from 220 to 700 nm. Theabsorbance corresponding to the RNA and the cyanine dye should then beused to calculate the quantity of RNA labeled and the efficiency of thecyanine dye incorporation.

Example 8 Hybridization with the Whole Human Genome Microarray forIdentification of Gene Expression Profiles for Prostate Cancer

Hybridization of fluorescent complementary RNA (cRNA) to the 60-meroligo microarray is a key step in gene expression profiling. By usingAgilent microarray technology, the gene expression profile of a specimenof interest can be determined, and simultaneously compare two RNAs (i.e.tumor vs. normal) that have been previously labeled with differentfluorescent dyes (cyanine 3 or cyanine 5).

Hybridization Procedure Using cRNA Labeled Targets

A) Preparation of 2×cRNA Target Solution to be Used on a 4x44K AgilentOligo Microarray

Before starting, and using powder-free gloves, the work area is cleanedthoroughly with either RNaseAway® (Sigma Cat. No. 83931) or 70% ethanol(70% 200proof ethanol and 30% pure water). It is very important that thework area, the materials and equipment used are very clean, dust- andRNAse-free.

The 10× Blocking Agent (Agilent Cat. No. 5188-5281) is prepared (ifusing stock tube for the first time) by using an RNAse-free filteredpipette tip to add 0.5 mL of RNAse-free (or DEPC water) to thelyophilized pellet, mixing gently by vortexing, and centrifuging for5-10 seconds. Once reconstituted with water, the 10× Blocking Agentshould be stored frozen at −20° C. for up to 2 months.

To a 0.2 mL RNAse-free PCR tube nuclease-free water is added, bringingto 52.8 μL volume.

Using an RNAse-free filtered pipette tip, 825 ng of cyanine 3-labeledcRNA and 825 ng of cyanine 5-labeled cRNA (or more if the labelingefficiency of one of them was lower in order to add approximatelyequivalent quantities of cyanine dyes in both) is added.

Using an RNAse-free filtered pipette tip, 11 μL of 10× Blocking Agent isadded.

This 2× Target solution may be quickly frozen in dry ice and stored inthe dark in a −80° C. freezer up to 1 month.

B) cRNA Fragmentation and Preparation of 1× Hybridization Solution

To the 52.8 μL 2×cRNA Target solution, 2.2 μL of 25× Fragmentationbuffer is added and is mixed gently by vortexing at a low speed before aquick centrifuge (5-10 seconds) to bring contents down from walls andtube lid.

The tube is incubated at 60° C. for 30 minutes in a thermal cycler suchas the PTC-200 from MJ Research. This incubation fragments the cRNA toideal size fragments that are optimal for hybridization. After theincubation, the tube is spun briefly in a microcentrifuge to drive thesample off the walls and lid.

55 μL of the 2×GE HI-RPM Hybridization Buffer is added and is then mixedwell by careful pipetting, taking care to avoid introducing bubbles. Thetube is then spun briefly in a microcentrifuge to drive the sample offthe walls and lid before being used immediately.

The sample is placed on ice and is loaded onto the array as soon aspossible.

C) Hybridization of Cyanine 3- and Cyanine 5-Labeled Samples to Agilent4×44 K Oligo Microarrays

As many assembled stainless steel hybridization chambers, gasket slidesand microarrays as necessary to complete the microarray hybridizationsare procured.

Before loading each microarray with the hybridization mixture, thesamples to be assayed are written down in a numerical order by writingdown the barcode number of the corresponding microarray and the position(Array 1_(—)1, 1_(—)2, 1_(—)3, 1_(—)4) where each sample was loaded.

The first gasket is placed on the base of the first hybridizationchamber base, making sure that the label of the gasket slide is facingup, and that it is well placed and flush with the chamber base. 100 μLof the hybridization solution is slowly drawn up from the first sampletube avoiding any bubbles, before “dispensing and dragging” it on thecenter of the gasket slide, so the solution will be slowly spread withthe pipet tip throughout the gasket slide while dispensing it, butleaving approximately 2-3 mm space between the solution and the gasketthat surrounds it.

Once the solution is dispensed, the hybridization chamber base with thegasket slide is not moved, and the microarray is placed over it as soonas possible.

The appropriate Agilent oligo microarray is removed from its packagingusing clean, powder-free gloves. To avoid damaging the microarraysurface, only the area where the barcode is placed and by the ends iswhere the microarray should be handled (a pair of teflon-coated, slantedtip forceps can also be helpful when handling the microarrays andplacing them over the gasket slide). It also helps removing themicroarray from the plastic package while the numeric side is facing up(“Agilent side is down”), since it'must be placed in this direction andit is easier to confirm that the right array (with the correct barcodenumber) is being assigned to that sample.

The array is carefully lowered and aligned with the 4 guide posts on thechamber base. Once aligned and slightly over (and parallel to) thegasket slide, the microarray slide is gently placed against the gasketslide to complete the sandwiched slide pair. The slides are quicklyassessed to assure they are completely aligned and that the oligomicroarray is not ajar.

The stainless steel chamber cover is placed onto the sandwiched slides,and then the clamp assembly is slid into place, until it comes to astopping point in the middle of the chamber base and cover pair. Thethumbscrew is tightened by turning it clockwise until it is fullyhandtight (without overtightening or using tools, as this may damage theparts and break the glass gasket slide and microarray.)

The chamber assembly is held vertically, and rotated slowly it clockwise2-3 times in order to allow the hybridization solution to wet the gasketand the microarray. The sandwiched slides are inspected for bubbleformation as a large mixing bubble should have formed. If stray, mixingbubbles are present and do not move as the chamber rotates, gently tapthe chamber against your hand or other surface, and rotate chamber again(while in vertical position) to determine if the stationary bubbles arenow moving. It is important that the stationary bubbles are dislodgedbefore loading the assembled chamber into the hybridization rotator rackand oven.

Once all of the chambers are fully assembled, they are loaded into thehybridization rotator rack, ensuring the loaded hybridization chambersare in balance with others (can use an empty chamber as well) in theopposite position. The hybridization rotator rack is set to rotate at 10rpm and the hybridization is at 65° C. for 17 hours.

D. Wash with Stabilization and Drying Solution.

Gene Expression Wash Buffer 2 is prewarmed to 37° C. as follows: 1000 mLof Gene Expression Wash Buffer 2 is dispensed directly into a sterile1000-mL bottle, and is repeated until enough prewarmed Wash2 solutionfor the experiment is present. The 1000-mL bottle cap is tightend andplaced in a 37° C. water bath the night before arrays.

Cyanine 5 is susceptible to degradation by ozone, thus, the followingprocedure is typically performed if the ozone levels in the laboratoryexceed 5 ppb. (NOTE: Fresh Gene Expression Wash Buffer 1 and 2 should beused for each wash group (up to eight slides). The acetonitrile andStabilization and Drying Solution may be reused for washing of up tothree groups of slides.)

The Agilent Stabilization and Drying Solution contain an ozonescavenging compound dissolved in acetonitrile. The compound in solutionis present in saturating amounts and may precipitate from the solutionunder normal storage conditions. If the solution shows visibleprecipitation, warming of the solution redissolves the compound. Washingslides using Stabilization and Drying Solution showing visibleprecipitation typically has a profound adverse effect on microarrayperformance.

The solution is slowly warmed in a water bath or a vented conventionaloven at 40° C. in a closed container with sufficient head space to allowfor expansion. If needed, the solution may be gently mixed to obtain ahomogenous solution, under a vented fume hood away from open flames, orother sources of ignition. The solution is warmed only in a controlledand contained area that meets local fire code requirements.

After the precipitate is completely dissolved, the covered solution isleft at room temperature, allowing it to equilibrate to room temperateprior to use. (NOTE: The original container can be used to warm thesolution. The time needed to completely redissolve the precipitate isdependent on the amount of precipitate present, and may requireovernight warming if precipitation is heavy. The Stabilization andDrying solution should not be filtered).

The Stabilization and Drying Solution should be set-up in a fume hood.Wash 1 and Wash 2 set-up areas should be placed close to, or preferablyin, the same fume hood. Gloves and eye/face protection should be used inevery step of the warming procedures.

The slide-staining dish #1 is completely filled with Gene ExpressionWash Buffer 1 at room temperature. A slide rack is placed intoslide-staining dish #2. A magnetic stir bar is then added and theslide-staining dish #2 is filled with enough Gene Expression Wash Buffer1 at room temperature to cover the slide rack. This dish is placed on amagnetic stir plate.

The empty dish #3 is placed on the stir plate and a magnetic stir bar isadded. The pre-warmed (37° C.) Gene Expression Wash Buffer 2 is notadded until the first wash step has begun.

The slide-staining dish #4 is filled approximately three-fourths fullwith acetonitrile, a magnetic stir bar is added and this dish is placedon a magnetic stir plate.

The slide-staining dish #5 is filled approximately three-fourths fullwith Stabilization and Drying Solution, a magnetic stir bar added andthis dish is placed on a magnetic stir plate.

The hybridization chamber is removed from incubator, and thehybridization chamber is prepared for disassembly. The hybridizationchamber assembly is placed on a flat surface and the thumbscrew isloosened, turning counter-clockwise. The clamp assembly is slid off andthe chamber cover removed.

With gloved fingers, the array-gasket sandwich is removed from thechamber base by grabbing the slides from their ends. Keeping themicroarray slide numeric barcode facing up, the sandwich is quicklytransferred to slide-staining dish #1.

Without letting go of the slides, the array-gasket sandwich is submergedinto slide-staining dish #1 containing Gene Expression Wash Buffer 1.With the sandwich completely submerged in Gene Expression Wash Buffer 1,the sandwich is pried open from the barcode end only:

One of the blunt ends of the forceps is slipped between the slides, theforeceps are turned gently upwards or downwards to separate the slides,letting the gasket slide drop to the bottom of the staining dish. Themicroarray slide is removed and placed into a slide rack in theslide-staining dish #2 containing Gene Expression Wash Buffer 1 at roomtemperature. Exposure of the slide to air should be minimized and onlythe barcode portion of the microarray slide or its edges should betouched.

When all slides in the group are placed into the slide rack inslide-staining dish #2, stirring is started using setting 4 for 1minute. During this wash step, Gene Expression Wash Buffer 2 is removedfrom the 37° C. water bath and is poured into the Wash 2 dish. The sliderack is transferred to slide-staining dish #3 containing Gene ExpressionWash Buffer 2 at elevated temperature and is stirred using setting 4 for1 minute.

The slide rack from Gene Expression Wash Buffer 2 is removed and therack is tilted slightly to minimize wash buffer carry-over. The sliderack is immediately transferred the to slide-staining dish #4 containingacetonitrile and is stirred using setting 4 for 30 seconds.

The slide rack is transferred to dish #5 filled with Stabilization andDrying Solution and is stirred using setting 4 for 1 minute.

The slide rack is slowly removed to minimize droplets on the slides. Itshould take 5 to 10 seconds to remove the slide rack. The used GeneExpression Wash Buffer 1 and Gene Expression Wash Buffer 2 arediscarded.

The slides are scanned immediately to minimize the impact ofenvironmental oxidants on signal intensities. If necessary, store slidesin orange slide boxes in a N2 purge box, in the dark.

To scan the microarray slides, the scanner is turned on and after a fewminutes the Agilent Scanner control is opened. The number of slides tobe scanned (up to 48) is selected and after highlighting the rows thatcorrespond to the slots to be scanned, Browse is selected and the outputpath or location where the image files will be saved is chosen.

To change any settings, click Settings>Modify Default Settings. A windowpops up from which you can change the setting. The scanning resolutionshould be set up for 5 mm. The scanner reads the barcode andautomatically names each file with that number.

When scanner status shows: “Scanner ready”, click Scan and each arraytakes approximately 7 minutes to be scanned. After all scans arefinished, a report will automatically appear listing all serial numbersand the status of the scan (successful or not).

The most commonly overexpressed genes is shown in FIG. 1A. In anotherstudy, the top 100 overexpressed genes were identified, and of those,the genes overexpressed in at least 5 of 6 samples were determined andis shown in FIG. 1B. An example of the results of the prostate cancersamples are shown in FIG. 2.

Example 9 Generating Product Values for Characterizing Prostate Cancer

A product value was determined by combining of miR-141 values with PSAvalues obtained from a subject's blood sample to create a product valueused to detect prostate cancer. Data on the serum PSA levels and miR-141levels from 25 men with metastatic prostate cancer and from 25 normalmen was obtained from Mitchell et al., PNAS Jul. 29, 2008 Vol 105 No. 30p. 10513-10518. The product value was determined by multiplying themiR-141 copy number by the PSA level (FIG. 5A).

The mean number of copies per microliter of serum of miR-141 from themen with prostate cancer is 15,648 with a 95% confidence interval aboutthe mean of +/−10,431 copies per microliter. The mean number of copiesper microliter of serum of miR-141 from men without prostate cancer is560 with a 95% confidence interval of the mean of +/−223 copies permicroliter (FIG. 5B). There is a clear differentiation of men withprostate cancer from normal men without prostate cancer.

The product value provides a novel analysis of data by using the numberof miR-141 copies and the PSA values for a subject that is predictive ofprostate cancer. The product value separates the men with prostatecancer from the men without prostate cancer with 100% sensitivity and100% specificity.

Various modifications of the invention, in addition to those describedherein, will be apparent to those skilled in the art from the foregoingdescription. Such modifications are also intended to fall within thescope of the appended claims. Each reference cited in the presentapplication is incorporated herein by reference in its entirety.

1. A method for characterizing a prostate cancer comprising: (a)determining an expression level of one or more miRNAs in a biologicalsample of a subject; and (b) determining a PCA3 score from a biologicalsample of said subject, wherein said PCA3 score is a ratio between anexpression level of PCA3 and an expression level of PSA; and, (c)characterizing said prostate cancer based on at least a subset of saidmiRNAs and said PCA3 score.
 2. The method of claim 1, wherein a singlebiological sample is used for steps (a) and (b).
 3. The method of claim1, wherein said prostate cancer is characterized by classifying saidcancer as benign, when said level of miRNA is less than about 3000copies per microliter and said PCA3 score is less than about
 35. 4. Themethod of claim 1, wherein said prostate cancer is characterized byclassifying said cancer as malignant, when said level of miRNA isgreater than about 9000 copies per microliter and said PCA3 score isgreater than about
 35. 5. A method for characterizing a cancer in asubject comprising: (a) determining an expression level of each of aplurality of miRNAs in a biological sample of said subject, and (b)characterizing said cancer based on said expression level of each ofsaid plurality of miRNAs, wherein said characterizing in (b) is withincreased sensitivity or specificity as compared to characterizing bydetecting an expression level of less than each of said plurality ofmiRNAs.
 6. The method of claim 5, wherein said plurality comprises atleast 10 miRNAs.
 7. The method of claim 5, wherein at least a subset ofsaid plurality of miRNAs is selected from Table
 1. 8. The method ofclaim 5, wherein at least a subset of said plurality of miRNAs isselected from the group consisting of: miR-629, miR-67′-3p, miR-9,miR-491, miR-182, miR125a-3p, miR-324-5p, miR-148b, miR-222, miR-141,miR-99, miR-101, miR-130, miR-135, miR-148, miR-182, miR-186, miR-206,miR-320, miR-374, miR-433, miR-496, miR-517, miR-590, miR-620, miR-768,miR-223, miR-203, miR-199, miR-519, miR-302, miR-30, miR-20, miR-200,miR-23, miR-181, miR-548 and miR-370.
 9. A method of classifying acancer as benign comprising: (a) determining an expression level of oneor more miRNAs in a biological sample of a subject; and (b) classifyingsaid cancer as benign when less than about 3000 copies per microliter ofat least a subset of said miRNAs is detected in said sample.
 10. Amethod of classifying a cancer as malignant comprising: (a) determiningan expression level of one or more miRNAs in a biological sample of asubject; and (h) classifying said cancer as malignant when greater thanabout 9000 copies per microliter of at least a subset of said miRNAs isdetected in said sample.
 11. The method of claim 9 or 10, furthercomprising selecting a therapy or treatment regimen based on saidclassification.
 12. The method of claim 9 or 10, wherein a result ofsaid classifying is transmitted over a network.
 13. A method ofcharacterizing a cancer comprising: determining an expression level ofone or more miRNAs in a first biological sample of said subject, whereinif between about 1000 to about 4500 copies per microliter of at least asubset of said miRNA in said sample are detected, a second biologicalsample is obtained.
 14. The method of claim 13, wherein said firstbiological sample is selected from the group consisting of: aheterogeneous cell sample, sputum, blood, blood cells, serum, biopsy,urine, peritoneal fluid, and pleural fluid.
 15. The method of claim 13,wherein said first biological sample is not a biopsy.
 16. The method ofclaim 13, wherein said second biological sample is a biopsy.
 17. Themethod of claim 13, wherein said second biological sample is analyzed byimmunohistochemistry, in situ hybridization (such as fluorescent in situhybridization), PCR, real-time PCR, microarray analysis or sequencing.18. The method of claim 5, 9, 10, or 13, wherein said cancer is anepithelial cancer.
 19. The method of claim 18, wherein said epithelialcancer is a breast, brain, pancreas, bone, liver, stomach, lung,colorectal, bladder, prostate or ovarian cancer.
 20. A method forcharacterizing a prostate cancer comprising: (a) determining anexpression level of one or more miRNAs in a biological sample of asubject; (b) determining an expression level of prostate-specificantigen (PSA) in a biological sample of a subject; and (c)characterizing said prostate cancer based on at least a subset of saidmiRNAs and said level of PSA.
 21. The method of claim 20, wherein asingle biological sample is used for steps (a) and (b).
 22. The methodof claim 20, wherein said expression level of said PSA is protein level.23. The method of claim 20, wherein said prostate cancer ischaracterized by classifying said prostate cancer as benign, when saidlevel of miRNA is less than about 3000 copies per microliter and saidPSA level is less than about 3 ng/ml.
 24. The method of claim 20,wherein said prostate cancer is characterized by classifying saidprostate cancer as malignant, when said level miRNA is greater thanabout 9000 copies per microliter and said PSA level is greater thanabout 4 ng/ml.
 25. The method of claim 20, further comprisingmultiplying an expression level of one of said miRNAs with said level ofPSA to obtain a product value, wherein said product value is used forcharacterizing said prostate cancer.
 26. The method of claim 25, whereinsaid miRNA is miR-141.
 27. The method of claim 25, wherein saidcharacterizing is with a sensitivity of at least about 75%.
 28. Themethod of claim 25, wherein said characterizing is with a specificity ofat least about 75%.
 29. The method of claim 25, wherein said prostatecancer is characterized by classifying said prostate cancer as benignwhen said product value is less than about
 1500. 30. The method of claim23 or 29, wherein an additional biological sample from said subject isnot obtained.
 31. The method of claim 25, wherein said prostate canceris characterized by classifying said prostate cancer as malignant, whensaid product value is greater than about
 1500. 32. The method of claim24 or 31, wherein an additional biological sample from said subject isobtained.
 33. The method of claim 32, wherein said additional biologicalsample is a biopsy.
 34. The method of claim 32, wherein said additionalbiological sample is analyzed by immunohistochemistry, in situhybridization (such as fluorescent in situ hybridization), PCR,real-time PCR, microarray analysis or sequencing.
 35. The method ofclaim 1, 9, 10, 13, or 20, wherein at least a subset of said miRNAs isselected from Table
 1. 36. The method of claim 1, 9, 10, 13, or 20,wherein at least a subset of said miRNAs is selected from the groupconsisting of: miR-629, miR-671-3p, miR-9, miR-491, miR-182, miR125a-3p,miR-324-5p, miR-148b, miR-222, miR-141, miR-99, miR-101, miR-130,miR-135, miR-148, miR-182, miR-186, miR-206, miR-320, miR-374, miR-433,miR-496, miR-517, miR-590, miR-620, miR-768, miR-223, miR-203, miR-199,miR-519, miR-302, miR-30, miR-20, miR-200, miR-23, miR-29, miR-181,miR-548 and miR-370.
 37. A method for characterizing a prostate cancerin a subject comprising: (a) determining an expression level of one ormore miRNAs in a biological sample of a subject, wherein at least asubset of said miRNAs is selected from the group consisting of: miR-629,miR-671-3p, miR-9, miR-491, miR-182, miR125a-3p, miR-324-5p, miR-148b,and miR-222, and (b) characterizing said prostate cancer based on saidexpression level in (a).
 38. The method of claim 37, further comprisingdetecting miR-141.
 39. The method of claim 37, wherein at least 2 ofsaid miRNAs in (a) is selected.
 40. The method of claim 37, wherein atleast 5 of said miRNAs in (a) is selected.
 41. The method of claim 1, 5,9, 10, 13, 20, or 37, wherein said biological sample is selected fromthe group consisting of a heterogeneous cell sample, sputum, blood,blood cells, serum, biopsy, urine, peritoneal fluid, and pleural fluid.42. The method of claim 1, 5, 13, 20, or 37, wherein a result of saidcharacterizing is transmitted over a network.
 43. The method of claim 9or 10, wherein a result of said classifying is transmitted over anetwork.
 44. A detection system configured to assess two or more miRNAsselected from the group consisting of: miR-629, miR-671-3p, miR-9,miR-491, miR-182, miR125a-3p, miR-324-5p, miR-148b, miR-222, andmiR-141.
 45. The detection system of claim 44, wherein said systemcomprises a set of probes that selectively hybridizes to said two ormore miRNAs.
 46. The detection system of claim 44, wherein said systemcomprises a probe for PSA.
 47. The detection system of claim 44, whereinsaid system comprises a probe for PCA3.
 48. A kit comprising a set ofprobes that selectively hybridizes to two or more miRNAs selected fromthe group consisting of: miR-629, miR-671-3p, miR-9, miR-491, miR-182,miR125a-3p, miR-324-5p, miR-148h, miR-222, and miR-141.
 49. The kit ofclaim 48, wherein each of said probes is coupled to a substrate.
 50. Thekit of claim 48, further comprising a probe for PSA.
 51. The kit ofclaim 48, further comprising a probe for PCA3.
 52. The kit of claim 48,further comprising a reagent for detecting PSA protein.